Summary
Imaging
Debian Med image processing and visualization packages
This metapackage will install Debian packages which might be useful in
medical image processing and visualization.
On one hand, it installs several packages supporting various image file
formats and image management, like DICOM (Digital Imaging and
Communications in Medicine) which is the de-facto standard for medical
image management, and NIFTI. On the other hand, it provides a variety of
software packages that can be used for visualization and for image processing
- either from a graphical user interface, the command line, or implemented in
workflows.
Description
For a better overview of the project's availability as a Debian package, each head row has a color code according to this scheme:
If you discover a project which looks like a good candidate for Debian Med
to you, or if you have prepared an unofficial Debian package, please do not hesitate to
send a description of that project to the Debian Med mailing list
Links to other tasks
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Debian Med Imaging packages
Official Debian packages with high relevance
amide
software for Medical Imaging
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Versions of package amide |
Release | Version | Architectures |
stretch | 1.0.5-7 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.0.5-12 | amd64,arm64,armhf,i386 |
sid | 1.0.6-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1.0.6-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 1.0.5-2 | amd64,armel,armhf,i386 |
bookworm | 1.0.6-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.0.5-15 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package amide: |
field | medicine, medicine:imaging |
role | program |
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License: DFSG free
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AMIDE: (Amide's a Medical Imaging Data Examiner)
AMIDE is a tool for viewing and analyzing medical image data sets.
It's capabilities include the simultaneous handling of multiple data
sets imported from a variety of file formats, image fusion, 3D region
of interest drawing and analysis, volume rendering, and rigid body
alignments.
Amide imports most clinical DICOM files (using the DCMTK library).
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ants
advanced normalization tools for brain and image analysis
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Versions of package ants |
Release | Version | Architectures |
sid | 2.4.3+dfsg-1 | amd64 |
trixie | 2.4.3+dfsg-1 | amd64 |
jessie | 2.1.0~rc2+git3-g9103999-4 | amd64,i386 |
stretch | 2.1.0-5 | amd64,i386 |
upstream | 2.5.4 |
Debtags of package ants: |
field | medicine:imaging |
interface | commandline |
role | program |
science | calculation |
scope | application |
works-with | file, image, image:raster |
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License: DFSG free
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Advanced Normalization Tools (ANTS) is an ITK-based suite of
normalization, segmentation and template-building tools for
quantitative morphometric analysis. Many of the ANTS registration
tools are diffeomorphic, but deformation (elastic and BSpline)
transformations are available. Unique components of ANTS include
multivariate similarity metrics, landmark guidance, the ability to
use label images to guide the mapping and both greedy and space-time
optimal implementations of diffeomorphisms. The symmetric
normalization (SyN) strategy is a part of the ANTS toolkit as is
directly manipulated free form deformation (DMFFD).
This package provides environment-modules configuration.
Use 'module load ants' to make all cmdline tools available in your shell.
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bart
tools for computational magnetic resonance imaging
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Versions of package bart |
Release | Version | Architectures |
sid | 0.9.00-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 0.9.00-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 0.6.00-3+deb11u1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 0.8.00-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 0.4.04-2 | amd64,arm64,armhf,i386 |
stretch | 0.4.00-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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The Berkeley Advanced Reconstruction Toolbox (BART) is a free and
open-source image-reconstruction framework for Computational Magnetic
Resonance Imaging. It consists of a programming library and a toolbox
of command-line programs. The library provides common operations on
multi-dimensional arrays, Fourier and wavelet transforms, as well as
generic implementations of iterative optimization algorithms. The
command-line tools provide direct access to basic operations on
multi-dimensional arrays as well as efficient implementations of
many calibration and reconstruction algorithms for parallel imaging,
compressed sensing, and machine learning.
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bart-view
viewer for multi-dimensional complex-valued data
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Versions of package bart-view |
Release | Version | Architectures |
buster | 0.1.00-2 | amd64,arm64,armhf,i386 |
bullseye | 0.1.00-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 0.2.00-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 0.3.00-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 0.3.00-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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The Berkeley Advanced Reconstruction Toolbox (BART) is a free and
open-source image-reconstruction framework for Computational Magnetic
Resonance Imaging.
This package provides an image viewer as an optional component of
the BART framework. The viewer is designed for multi-dimensional
complex-valued data.
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biosig-tools
format conversion tools for biomedical data formats
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Versions of package biosig-tools |
Release | Version | Architectures |
buster | 1.9.3-2 | amd64,arm64,armhf,i386 |
bookworm | 2.5.0-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 2.6.1-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 2.6.1-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 2.1.2-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 1.3.0-2.2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.3.0-2 | amd64,armel,armhf,i386 |
Debtags of package biosig-tools: |
interface | commandline |
role | program |
use | converting |
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License: DFSG free
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Based on BioSig library, this package provides command line
tools, such as
- save2gdf: converter between different file formats, including but
not limited to SCP-ECG(EN1064), HL7aECG (FDA-XML), GDF, EDF,
BDF, CWFB.
- biosig2gdf: converts biosig data files into GDF, to simplify
parsing and loading by scripting languages (e.g. loadgdf.{py,r})
- rec2bin, bin2rec, heka2itx, save2aecg, save2scp: several converter
tools based on save2gdf
- biosig_fhir: packs biosignal data into HL7/FHIR binary template file.
- physicalunits: converter for encoding and decoding of physical
units according to ISO 11073-10101
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camitk-imp
workbench application for the CamiTK library
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Versions of package camitk-imp |
Release | Version | Architectures |
stretch | 4.0.4-2 | amd64,i386 |
jessie | 3.3.2-2 | amd64,armel,armhf,i386 |
sid | 5.2.0-2 | amd64 |
trixie | 5.2.0-2 | amd64 |
bullseye | 4.1.2-4 | amd64,i386 |
buster | 4.1.2-3 | amd64,i386 |
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License: DFSG free
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CamiTK helps researchers and clinicians to easily and rapidly collaborate in
order to prototype CAMI applications, that feature medical images,
surgical navigation and biomechanical simulations.
camitk-imp is the CamiTK workbench application where you can test
all available extensions for prototyping.
It provides an easy and interactive access to all available data and
algorithm parameters, including the one you build yourself using
the CamiTK SDK.
For example, camitk-imp can visualize medical images from a lot of different
(standard) formats, offers image processing and segmentation algorithms to
reconstruct a mesh geometry and run a biomechanical simulation.
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caret
??? missing short description for package caret :-(
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Versions of package caret |
Release | Version | Architectures |
jessie | 5.6.4~dfsg.1-3 | amd64,armel,armhf,i386 |
Debtags of package caret: |
role | program |
uitoolkit | qt |
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License: DFSG free
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ctn
Central Test Node, a DICOM implementation for medical imaging
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Versions of package ctn |
Release | Version | Architectures |
bookworm | 3.2.0~dfsg-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 3.2.0~dfsg-5 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 3.2.0~dfsg-2 | amd64,armel,armhf,i386 |
sid | 3.2.0~dfsg-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 3.2.0~dfsg-6 | amd64,arm64,armhf,i386 |
trixie | 3.2.0~dfsg-8 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 3.2.0~dfsg-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package ctn: |
field | medicine:imaging |
interface | commandline, web, x11 |
role | program |
scope | application |
uitoolkit | athena, motif |
use | converting |
works-with | db, image, image:raster |
x11 | application |
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License: DFSG free
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DICOM is the standard for image storage, annotation, and networking.
It is used widely for medical imaging. The Central Test Node software (CTN)
provides an implementation of this standard.
This package includes the binary and run-time configuration files for CTN.
Please cite:
S.M. Moore, S.A. Hoffman and D.E. Beecher:
DICOM Shareware: A Public Implementation of the DICOM Standard
2165:772–781
(1994)
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ctsim
Computed tomography simulator
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Versions of package ctsim |
Release | Version | Architectures |
sid | 6.0.2-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 6.0.2-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 6.0.2-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 6.0.2-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 6.0.2-2 | amd64,arm64,armhf,i386 |
stretch | 5.2.0-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 5.2.0-2 | amd64,armel,armhf,i386 |
Debtags of package ctsim: |
field | biology |
interface | 3d, commandline |
role | program |
scope | application |
uitoolkit | wxwidgets |
use | viewing |
works-with | 3dmodel |
x11 | application |
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License: DFSG free
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CTSim provides an interactive computed tomography simulator. Computed
tomography is the technique of estimating the interior of an object
by measuring x-ray absorption through that object.
CTSim has both command-line tools and a graphical user interface.
CTSim has very educational trace modes for viewing the data
collection simulation as well as the reconstruction.
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dcm2niix
next generation DICOM to NIfTI converter
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Versions of package dcm2niix |
Release | Version | Architectures |
buster | 1.0.20181125-1 | amd64,arm64,armhf,i386 |
stretch | 1.0.20161101-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 1.0.20240202-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64 |
trixie | 1.0.20240202-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64 |
bookworm | 1.0.20220720-1+deb12u1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.0.20201102-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
upstream | 1.0.20241211 |
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License: DFSG free
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dcm2niix is the successor of dcm2nii, a popular tool for converting images
from the complicated formats used by scanner manufacturers (DICOM, PAR/REC)
to the simpler NIfTI format used by many scientific tools. It works for all
modalities (CT, MRI, PET, SPECT) and sequence types.
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dcmtk
OFFIS DICOM toolkit command line utilities
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Versions of package dcmtk |
Release | Version | Architectures |
stretch | 3.6.1~20160216-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bullseye | 3.6.5-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye-backports | 3.6.7-6~bpo11+1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 3.6.7-9~deb12u1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster-security | 3.6.4-2.1+deb10u1 | amd64,arm64,armhf,i386 |
sid | 3.6.8-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 3.6.8-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 3.6.0-15+deb8u1 | amd64,armel,armhf,i386 |
jessie-security | 3.6.0-15+deb8u1 | amd64,armel,armhf,i386 |
buster | 3.6.4-2.1 | amd64,arm64,armhf,i386 |
Debtags of package dcmtk: |
interface | commandline |
role | program |
scope | utility |
use | converting, downloading |
works-with | image, image:raster |
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License: DFSG free
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DCMTK includes a collection of libraries and applications for examining,
constructing and converting DICOM image files, handling offline media,
sending and receiving images over a network connection, as well as
demonstrative image storage and worklist servers.
This package contains the DCMTK utility applications.
Note: This version was compiled with libssl support.
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dicom3tools
DICOM medical image files manipulation and conversion tools
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Versions of package dicom3tools |
Release | Version | Architectures |
bullseye-backports | 1.00~20220120135102-1~bpo11+1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 1.00~20140902075059-1 | amd64,armel,armhf,i386 |
stretch | 1.00~20170109062447-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.00~20180803063840-1 | amd64,arm64,armhf,i386 |
bullseye | 1.00~20190724083540-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.00~20220618093127-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.00~20240118131615-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.00~20240118131615-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
upstream | 1.00~20241114112559 |
Debtags of package dicom3tools: |
field | medicine, medicine:imaging |
role | program |
use | converting |
works-with | image |
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License: DFSG free
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Command line utilities for creating, modifying, dumping and validating
files of DICOM attributes. Support conversion of some proprietary medical
image formats to DICOM. Can handle older ACR/NEMA format data, and some
proprietary versions of that such as SPI.
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dicomscope
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Versions of package dicomscope |
Release | Version | Architectures |
buster | 3.6.0-20 | all |
sid | 3.6.0-27 | all |
bullseye | 3.6.0-22 | all |
bookworm | 3.6.0-25 | all |
trixie | 3.6.0-27 | all |
jessie | 3.6.0-11 | amd64,armel,armhf,i386 |
stretch | 3.6.0-15 | all |
Debtags of package dicomscope: |
field | medicine, medicine:imaging |
role | program |
use | viewing |
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License: DFSG free
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DICOMscope is a free DICOM viewer which can display uncompressed, monochrome
DICOM images from all modalities and which supports monitor calibration
according to DICOM part 14 as well as presentation states.
DICOMscope offers a print client (DICOM Basic Grayscale Print Management)
which also implements the optional Presentation LUT SOP Class.
The development of this prototype was commissioned by the "Committee for the
Advancement of DICOM" and demonstrated at the European Congress of Radiology
ECR 1999. An enhanced version was developed for the "DICOM Display Consistency
Demonstration" at RSNA InfoRAD 1999.
The current release has been demonstrated at ECR 2001 and contains numerous
extensions, including a print server, support for encrypted DICOM
communication, digital signatures and structured reporting.
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fslview
??? missing short description for package fslview :-(
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Versions of package fslview |
Release | Version | Architectures |
jessie | 4.0.1-4 | amd64,armel,armhf,i386 |
Debtags of package fslview: |
interface | x11 |
made-of | html |
role | documentation, program |
scope | utility |
suite | debian |
uitoolkit | qt |
use | viewing |
x11 | application |
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License: DFSG free
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Please cite:
S.M. Smith, M. Jenkinson, M.W. Woolrich, C.F. Beckmann, T.E.J. Behrens, H. Johansen-Berg, P.R. Bannister, M. De Luca, I. Drobnjak, D.E. Flitney, R. Niazy, J. Saunders, J. Vickers, Y. Zhang, N. De Stefano, J.M. Brady and P.M. Matthews:
Advances in functional and structural MR image analysis and implementation as FSL.
(PubMed)
NeuroImage
23:208-219
(2004)
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gdf-tools
IO library for the GDF -- helper tools
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Versions of package gdf-tools |
Release | Version | Architectures |
sid | 0.1.3-11.1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 0.1.3-11.1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 0.1.3-11 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 0.1.3-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 0.1.2-2.1 | amd64,arm64,armhf,i386 |
stretch | 0.1.2-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 0.1.2-2 | amd64,armel,armhf,i386 |
Debtags of package gdf-tools: |
role | program |
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License: DFSG free
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GDF (General Dataformat for Biosignals) is intended to provide a generic
storage for biosignals, such as EEG, ECG, MEG etc.
This package provides the tool shipped with the library
(gdf_merger).
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ginkgocadx
Medical Imaging Software and complete DICOM Viewer
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Versions of package ginkgocadx |
Release | Version | Architectures |
buster | 3.8.8-1 | amd64,i386 |
stretch | 3.8.4-1 | amd64,i386 |
jessie | 3.7.0.1465.37+dfsg-1 | amd64,armel,armhf,i386 |
bullseye | 3.8.8-5 | amd64,i386 |
Debtags of package ginkgocadx: |
field | medicine, medicine:imaging |
role | program |
uitoolkit | gtk, wxwidgets |
use | viewing |
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License: DFSG free
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Ginkgo CADx provides a complete DICOM viewer solution with advanced
capabilities and support for extensions.
- Easy and customizable interface through profiles.
- Full featured DICOM image visualization.
- Complete tool set (measure, markers, text, ...).
- Multiple modalities support (Neurological, Radiological, Dermatological,
Ophthalmological, Ultrasound, Endoscopy, ...)
- Dicomization support from JPEG, PNG, GIF and TIFF.
- Full EMH integration support: HL7 standard and IHE compliant workflows.
- PACS Workstation (C-FIND, C-MOVE, C-STORE...)
- Extensible through custom extensions.
- Retinal image mosaic composition.
- Automatic retinal analysis diagnostics.
- Psoriasis automatic diagnostics.
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gwyddion
Scanning Probe Microscopy visualization and analysis tool
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Versions of package gwyddion |
Release | Version | Architectures |
stretch | 2.47-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bullseye | 2.57-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 2.38-2 | amd64,armel,armhf,i386 |
bookworm | 2.62-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 2.52-1 | amd64,arm64,armhf,i386 |
sid | 2.67-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 2.67-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package gwyddion: |
field | physics |
interface | x11 |
role | program |
science | visualisation |
scope | application |
uitoolkit | gtk |
use | analysing, viewing |
works-with | image, image:raster |
x11 | application |
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License: DFSG free
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Gwyddion is a modular program for Scanning Probe Microscopy (SPM) data
visualization and analysis. It is primarily intended for analysis of height
field data obtained by microscopy techniques like
- Atomic Force Microscopy (AFM),
- Magnetic Force Microscopy (MFM),
- Scanning Tunneling Microscopy (STM),
- Near-field Scanning Optical Microscopy (SNOM or NSOM)
and others. However, it can be used for arbitrary height field and
image analysis.
This package contains the main application and its modules. It also contains
a GNOME (and Xfce) thumbnailer which creates previews for all file types known
to Gwyddion.
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heudiconv
DICOM converter with support for structure heuristics
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Versions of package heudiconv |
Release | Version | Architectures |
trixie | 1.3.2-1 | all |
bookworm | 0.11.6-1 | all |
sid | 1.3.2-1 | all |
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License: DFSG free
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This is a flexible dicom converter for organizing brain imaging data into
structured directory layouts. It allows for flexible directory layouts and
naming schemes through customizable heuristics implementations.
It only converts the necessary dicoms, not everything in a directory.
It tracks the provenance of the conversion from dicom to nifti in w3c
prov format.
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imagej
Image processing program with a focus on microscopy images
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Versions of package imagej |
Release | Version | Architectures |
sid | 1.54g-1 | all |
buster | 1.52j-1 | all |
bullseye | 1.53g-2 | all |
bookworm | 1.53t-1 | all |
trixie | 1.54g-1 | all |
jessie | 1.49i+dfsg-1 | all |
stretch | 1.51i+dfsg-2 | all |
Debtags of package imagej: |
role | program |
use | analysing, editing, viewing |
works-with | image, image:raster |
works-with-format | gif, jpg, tiff |
|
License: DFSG free
|
It can display, edit, analyze, process, save and print 8-bit, 16-bit and
32-bit images. It can read many image formats including TIFF, GIF, JPEG,
BMP, DICOM, FITS and "raw". It supports "stacks", a series of images that
share a single window.
It can calculate area and pixel value statistics of user-defined
selections. It can measure distances and angles. It can create density
histograms and line profile plots. It supports standard image processing
functions such as contrast manipulation, sharpening, smoothing, edge
detection and median filtering.
Spatial calibration is available to provide real world dimensional
measurements in units such as millimeters. Density or gray scale
calibration is also available.
ImageJ is developed by Wayne Rasband (wayne@codon.nih.gov), is at the
Research Services Branch, National Institute of Mental Health, Bethesda,
Maryland, USA.
|
|
imagevis3d
desktop volume rendering application for large data
|
Versions of package imagevis3d |
Release | Version | Architectures |
buster | 3.1.0-7 | amd64,arm64,armhf,i386 |
stretch | 3.1.0-5 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 3.1.0-4 | amd64,armel,armhf,i386 |
Debtags of package imagevis3d: |
uitoolkit | qt |
|
License: DFSG free
|
ImageVis3D is a volume rendering application specifically designed to render
large data. This is achieved by splitting the dataset into multiple levels of
detail (LoD), with each level itself decomposed into multiple bricks (atomic
rendering primitive). Interaction occurs at the coarsest LoD, which can be
rendered instantaneously on almost all modern systems. After a configurable
delay, ImageVis3D will successively render finer levels of detail, until the
data are visible at their native resolution.
Development of ImageVis3D is sponsored by the NIH/NCRR Center for Integrative
Biomedical Computing (CIBC), and the DOE Visualization And Analytics Center for
Enabling Technologies (VACET).
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|
invesalius
3D medical imaging reconstruction software
|
Versions of package invesalius |
Release | Version | Architectures |
bullseye | 3.1.99994-1 | all |
stretch | 3.0.1-1 | all |
buster | 3.1.99992-3 | all |
sid | 3.1.99998-6 | all |
jessie | 3.0~b5-4 | all |
trixie | 3.1.99998-6 | all |
bookworm | 3.1.99998-4 | all |
|
License: DFSG free
|
InVesalius generates 3D medical imaging reconstructions based on a sequence of
2D DICOM files acquired with CT or MRI equipments. InVesalius is
internationalized (currently available in English, Portuguese, French,
Spanish, Turkish, Italian, Czesh, Japanese, Catalan, Korean, Romanian and
German) and provides several tools:
- DICOM support including: (a) ACR-NEMA version 1 and 2; (b) DICOM
version 3.0 (including various encodings of JPEG -lossless and lossy-, RLE)
- Image manipulation features (zoom, pan, rotation, brightness/contrast,
etc)
- Segmentation based on 2D slices
- Pre-defined threshold ranges according to tissue of interest
- Segmentation based on watershed
- Region growing segmentation
- Edition tools (similar to Paint Brush) based on 2D slices
- Semi-automatic segmentation based on Watershed
- 3D surface creation
- 3D surface connectivity tools
- 3D surface exportation (including: binary STL, OBJ, VRML, Inventor)
- High-quality volume rendering projection
- Pre-defined volume rendering presets
- Volume rendering crop plane
- Picture exportation (including: BMP, TIFF, JPG, PostScript, POV-Ray)
- Minimum, Maximum or Mean Intensity Projection, Maximum Intensity Difference
Accumulation and Contour based visualizations
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|
ismrmrd-tools
command-line tools for ISMRMRD
|
Versions of package ismrmrd-tools |
Release | Version | Architectures |
buster | 1.4.0-1 | amd64,arm64,i386 |
bullseye | 1.4.2.1-6 | amd64,arm64,armel,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 1.3.3-1 | amd64,arm64,armel,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 1.8.0-2 | amd64,arm64,armel,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.8.0-2 | amd64,arm64,armel,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.8.0-2 | amd64,arm64,armel,i386,mips64el,ppc64el,riscv64,s390x |
upstream | 1.14.2 |
|
License: DFSG free
|
The ISMRMRD format combines a mix of flexible data structures (XML header)
and fixed structures (equivalent to C-structs) to represent MRI data.
In addition, the ISMRMRD format also specifies an image header for storing
reconstructed images and the accompanying C++ library provides a convenient
way of writing such images into HDF5 files along with generic arrays for
storing less well defined data structures, e.g. coil sensitivity maps or
other calibration data.
This package provides the command-line tools.
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itksnap
semi-automatic segmentation of structures in 3D images
|
Versions of package itksnap |
Release | Version | Architectures |
jessie | 2.2.0-1.1 | amd64,armel,armhf,i386 |
buster | 3.6.0-3 | amd64,i386 |
bullseye | 3.6.0-5 | amd64,i386 |
stretch | 3.4.0-2 | amd64,i386 |
Debtags of package itksnap: |
field | medicine:imaging |
role | program |
|
License: DFSG free
|
SNAP provides semi-automatic segmentation of structures in medical
images (e.g. magnetic resonance images of the brain) using active
contour methods, as well as manual delineation and image navigation.
Noteworthy features are:
- Linked cursor for seamless 3D navigation
- Manual segmentation in three orthogonal planes at once
- Support for many different 3D image formats, including NIfTI
- Support for concurrent, linked viewing and segmentation of multiple images
- Limited support for color images (e.g., diffusion tensor maps)
- 3D cut-plane tool for fast post-processing of segmentation results
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king
interactive system for three-dimensional vector graphics
|
Versions of package king |
Release | Version | Architectures |
bookworm | 2.24+dfsg2-1 | all |
bullseye | 2.23.161103+dfsg1-4 | all |
buster | 2.23.161103+dfsg1-3 | all |
stretch | 2.23.161103+dfsg1-1 | all |
jessie | 2.21.120420+dfsg-1 | all |
sid | 2.24+dfsg2-2 | all |
trixie | 2.24+dfsg2-2 | all |
|
License: DFSG free
|
KiNG (Kinemage, Next Generation) is an interactive system for
three-dimensional vector graphics. It supports a set of graphics
primitives that make it suitable for many types of graphs, plots, and
other illustrations; although its first use was to display
macromolecular structures for biophysical research. KiNG builds on Mage,
JavaMage, and the "kinemage" (kinetic image) concept to deliver a
full-featured Java application with a user-friendly interface and
integrated editing features. The KiNG jar file can be used within a web
page as a Java applet or Java object to promote easy access to kinemages
or coordinate files from a web browser.
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libgdcm-tools
Grassroots DICOM tools and utilities
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Versions of package libgdcm-tools |
Release | Version | Architectures |
buster | 2.8.8-9 | amd64,arm64,armhf,i386 |
trixie | 3.0.24-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 3.0.24-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 3.0.8-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye-backports | 3.0.17-4~bpo11+1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 3.0.21-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 2.4.4-3+deb8u1 | amd64,armel,armhf,i386 |
stretch | 2.6.6-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package libgdcm-tools: |
field | medicine:imaging |
interface | commandline |
role | program |
scope | utility |
use | converting |
works-with | image, image:raster |
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License: DFSG free
|
Grassroots DiCoM is a C++ library for DICOM medical files. It is
automatically wrapped to python/C#/Java (using swig). It supports
RAW,JPEG (lossy/lossless),J2K,JPEG-LS, RLE and deflated.
Install this package for the gdcmanon, gdcmclean, gdcmconv, gdcmdiff,
gdcmdump, gdcmpap3, gdcmgendir, gdcmimg, gdcminfo, gdcmpdf, gdcmraw,
gdcmscanner, gdcmscu, gdcmtar, gdcmxml programs.
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medcon
Medical Image (DICOM, ECAT, ...) conversion tool
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Versions of package medcon |
Release | Version | Architectures |
bookworm | 0.23.0-gtk3+dfsg-1+deb12u1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 0.24.0-gtk3+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 0.13.0-2 | amd64,armel,armhf,i386 |
buster | 0.16.1+dfsg-1 | amd64,arm64,armhf,i386 |
bullseye | 0.16.3+dfsg-1+deb11u1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 0.14.1-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
trixie | 0.24.0-gtk3+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
upstream | 0.24.1-gtk3 |
Debtags of package medcon: |
field | biology |
interface | commandline |
role | program |
uitoolkit | gtk |
use | converting |
works-with | image, image:raster |
x11 | application |
|
License: DFSG free
|
This project stands for Medical Image Conversion. Released under the
(L)GPL, it comes with the full C-source code of the library, a
flexible command line utility and a neat graphical front-end using
the GTK+ toolkit. The currently supported formats are: Acr/Nema 2.0,
Analyze (SPM), DICOM 3.0, InterFile 3.3 and PNG.
The program also allows one to read unsupported files without
compression, to print pixel values or to extract/reorder specified
images. It is possible to retrieve the raw binary/ascii image arrays
or to write PNG for desktop applications.
This is the command line tool for batch processing.
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mia-tools
Command line tools for gray scale image processing
|
Versions of package mia-tools |
Release | Version | Architectures |
bullseye | 2.4.7-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 2.2.2-1 | amd64,i386 |
buster | 2.4.6-4 | amd64,arm64,armhf,i386 |
stretch | 2.4.3-5 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 2.4.7-13 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 2.4.7-11 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
Command lines tools to run general purpose image processing tasks on 2D
and 3D gray scale images, and basic operations on triangular meshes.
Supported image processing algorithms are image filtering, combining, image
registration, motion compensation for image series, and the estimation of
various statistics over images.
This package also contains the nipype interfaces for these command line tools.
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mia-viewit
??? missing short description for package mia-viewit :-(
|
Versions of package mia-viewit |
Release | Version | Architectures |
stretch | 1.0.4-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.0.1-1 | amd64,i386 |
bookworm | 1.0.5-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.0.5-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.0.5-2 | amd64,arm64,armhf,i386 |
Debtags of package mia-viewit: |
uitoolkit | gtk |
|
License: DFSG free
|
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mialmpick
Tools for landmark picking in 3D volume data sets
|
Versions of package mialmpick |
Release | Version | Architectures |
jessie | 0.2.10-2 | amd64,armel,armhf,i386 |
sid | 0.2.15-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 0.2.15-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 0.2.14-2 | amd64,arm64,armhf,i386 |
stretch | 0.2.13-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package mialmpick: |
uitoolkit | gtk |
|
License: DFSG free
|
This tool provides a simple 3D renderer that can visualize surfaces
directly from 3D volumes and can be used to set 3D landmarks.
It is best suited for CT data sets.
Please cite:
Gert Wollny, Fritjhof Kruggel, Thomas Hierl and Jörg Hendricks:
Assessment, validation, and visualisation of bony changes in crano-facial surgery
(eprint)
:459-464
(2004)
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minc-tools
MNI medical image format tools
|
Versions of package minc-tools |
Release | Version | Architectures |
jessie | 2.2.00-6 | amd64,armel,armhf,i386 |
sid | 2.3.00+dfsg-10 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 2.3.00+dfsg-10 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 2.3.00+dfsg-10 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 2.3.00+dfsg-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 2.3.00+dfsg-3 | amd64,arm64,armhf,i386 |
stretch | 2.3.00+dfsg-1.1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package minc-tools: |
field | medicine, medicine:imaging |
interface | commandline |
role | program |
scope | utility |
use | analysing, converting |
works-with | image, image:raster |
|
License: DFSG free
|
This package contains tools to manipulate MINC files.
The Minc file format is a highly flexible medical image file format
built on top of the NetCDF generalized data format. The format is
simple, self-describing, extensible, portable and N-dimensional, with
programming interfaces for both low-level data access and high-level
volume manipulation. On top of the libraries is a suite of generic
image-file manipulation tools. The format, libraries and tools are
designed for use in a medical-imaging research environment: they are
simple and powerful and make no attempt to provide a pretty interface
to users.
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mricron
magnetic resonance image conversion, viewing and analysis
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Versions of package mricron |
Release | Version | Architectures |
buster | 0.20140804.1~dfsg.1-3 | amd64,arm64,armhf,i386 |
sid | 1.2.20211006+dfsg-6 | amd64,arm64,armel,armhf,i386,ppc64el |
jessie | 0.20140804.1~dfsg.1-1 | amd64,armel,armhf,i386 |
trixie | 1.2.20211006+dfsg-6 | amd64,arm64,armel,armhf,i386,ppc64el |
bookworm | 1.2.20211006+dfsg-4 | amd64,arm64,armel,armhf,i386,ppc64el |
stretch | 0.20140804.1~dfsg.1-2 | amd64,arm64,armel,armhf,i386 |
bullseye | 1.0.20190902+dfsg-2 | amd64,arm64,armel,armhf,i386,ppc64el |
Debtags of package mricron: |
uitoolkit | gtk |
|
License: DFSG free
|
This is a GUI-based visualization and analysis tool for (functional) magnetic
resonance imaging. MRIcron can be used to create 2D or 3D renderings of
statistical overlay maps on brain anatomy images. Moreover, it aids drawing
anatomical regions-of-interest (ROI), or lesion mapping, as well as basic
analysis of functional timeseries (e.g. creating plots of peristimulus
signal-change).
In addition to 'mricron', this package also provides 'dcm2nii' that supports
converting DICOM and PAR/REC images into the NIfTI format, and 'npm' for
non-parametric data analysis.
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mrtrix3
diffusion-weighted MRI white matter tractography
|
Versions of package mrtrix3 |
Release | Version | Architectures |
trixie | 3.0.4-1 | amd64,arm64 |
sid | 3.0.4-1 | amd64,arm64 |
bookworm | 3.0.3-3 | amd64,arm64 |
bullseye | 3.0~rc3+git135-g2b8e7d0c2-5 | amd64,arm64 |
buster | 3.0~rc3+git135-g2b8e7d0c2-3 | amd64,arm64,i386 |
|
License: DFSG free
|
Set of tools to perform diffusion-weighted MRI white matter tractography of the
brain in the presence of crossing fibres, using Constrained Spherical
Deconvolution, and a probabilisitic streamlines algorithm. Magnetic resonance
images in DICOM, ANALYZE, or uncompressed NIfTI format are supported.
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nifti-bin
tools shipped with the NIfTI library
|
Versions of package nifti-bin |
Release | Version | Architectures |
trixie | 3.0.1-9.1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 3.0.1-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 3.0.1-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 2.0.0-2 | amd64,armel,armhf,i386 |
buster | 2.0.0-3 | amd64,arm64,armhf,i386 |
stretch | 2.0.0-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 3.0.1-9.1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package nifti-bin: |
field | medicine, medicine:imaging |
interface | commandline |
role | program, shared-lib |
scope | utility |
use | checking, converting |
|
License: DFSG free
|
Niftilib is a set of i/o libraries for reading and writing files in the
NIfTI-1 data format. NIfTI-1 is a binary file format for storing medical
image data, e.g. magnetic resonance image (MRI) and functional MRI (fMRI)
brain images.
This package provides the tools that are shipped with the library
(nifti_tool, nifti_stats and nifti1_test).
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odil
C++11 library for the DICOM standard (application)
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Versions of package odil |
Release | Version | Architectures |
bullseye | 0.12.1-1 | all |
buster | 0.10.0-3 | all |
stretch | 0.7.3-1 | all |
bookworm | 0.12.2-2 | all |
trixie | 0.12.2-5 | all |
sid | 0.12.2-5 | all |
upstream | 0.13.0 |
|
License: DFSG free
|
Odil leverages C++ constructs to provide a user-friendly API of the
different parts of the DICOM standard. Included in Odil are exception-based
error handling, generic access to datasets elements, standard JSON and XML
representation of datasets, and generic implementation of messages, clients
and servers for the various DICOM protocols.
This package contains the command-line application.
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odin
develop, simulate and run magnetic resonance sequences
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Versions of package odin |
Release | Version | Architectures |
trixie | 2.0.5-7 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 2.0.5-7 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 2.0.4-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 2.0.5-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 1.8.8-1 | amd64,armel,armhf,i386 |
buster | 2.0.3-1 | amd64,arm64,armhf,i386 |
|
License: DFSG free
|
ODIN is a framework for magnetic resonance imaging (MRI).
It covers the whole toolchain of MRI, from low-level data acquisition
to image reconstruction. In particular, it aims at rapid prototyping
of MRI sequences. The sequences can be programmed using a high-level,
object oriented, C++ programming interface. It provides advanced
sequence analysis tools, such as interactive plotting of k-space
trajectories, a user interface for a fast compile-link-test cycle
and a powerful MRI simulator which supports different virtual samples.
For fast and flexible image reconstruction, ODIN contains a highly
customizable, multi-threaded data-processing framework.
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openslide-tools
Manipulation and conversion tools for OpenSlide
|
Versions of package openslide-tools |
Release | Version | Architectures |
buster | 3.4.1+dfsg-4 | amd64,arm64,armhf,i386 |
jessie | 3.4.0-1 | amd64,armel,armhf,i386 |
stretch | 3.4.1+dfsg-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 3.4.1+dfsg-7 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 3.4.1+dfsg-7 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 3.4.1+dfsg-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 3.4.1+dfsg-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
upstream | 4.0.0 |
Debtags of package openslide-tools: |
role | program |
scope | utility |
|
License: DFSG free
|
OpenSlide is a C library that provides a simple interface to read whole-slide
images also known as virtual slides.
Whole-slide images, also known as virtual slides, are large, high resolution
images used in digital pathology. Reading these images using standard image
tools or libraries is a challenge because these tools are typically designed
for images that can comfortably be uncompressed into RAM or a swap file.
Whole-slide images routinely exceed RAM sizes, often occupying tens of
gigabytes when uncompressed. Additionally, whole-slide images are typically
multi-resolution, and only a small amount of image data might be needed at a
particular resolution.
This library currently supports:
- Aperio (.svs, .tif)
- Hamamatsu (.vms, .vmu, .ndpi)
- Leica (.scn)
- MIRAX (.mrxs)
- Sakura (.svslide)
- Trestle (.tif)
- Generic tiled TIFF (.tif)
This package contains command line tools for file manipulation.
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orthanc
Lightweight, RESTful DICOM server for medical imaging
|
Versions of package orthanc |
Release | Version | Architectures |
buster | 1.5.6+dfsg-1 | amd64,arm64,armhf,i386 |
jessie | 0.8.4+dfsg-1 | amd64,armel,armhf,i386 |
stretch | 1.2.0+dfsg-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster-security | 1.5.6+dfsg-1+deb10u1 | amd64,arm64,armhf,i386 |
bullseye | 1.9.2+really1.9.1+dfsg-1+deb11u1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye-security | 1.9.2+really1.9.1+dfsg-1+deb11u1 | amd64,arm64,armhf,i386 |
bookworm | 1.10.1+dfsg-2+deb12u1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm-security | 1.10.1+dfsg-2+deb12u1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.12.4+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.12.5+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
|
License: DFSG free
|
Orthanc aims at providing a simple, yet powerful DICOM server for
medical imaging. Orthanc can turn any computer running Windows or
Linux into a Vendor Neutral Archive (in other words, a mini-PACS
system). Its architecture is lightweight, meaning that no complex
database administration is required, nor the installation of
third-party dependencies.
What makes Orthanc unique is the fact that it provides a RESTful
API. Thanks to this major feature, it is possible to drive Orthanc
from any computer language. The DICOM tags of the stored medical
images can be downloaded in the JSON file format. Furthermore,
standard PNG images can be generated on-the-fly from the DICOM
instances by Orthanc.
Orthanc lets its users focus on the content of the DICOM files,
hiding the complexity of the DICOM format and of the DICOM protocol.
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orthanc-wsi
Whole-slide imaging support for Orthanc (digital pathology)
|
Versions of package orthanc-wsi |
Release | Version | Architectures |
trixie | 2.1+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 0.6-2 | amd64,arm64,armhf,i386 |
bookworm | 1.1-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.0-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 3.0+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
|
License: DFSG free
|
Orthanc-WSI brings support of whole-slide imaging for digital
pathology into Orthanc, the lightweight, RESTful Vendor Neutral
Archive for medical imaging.
This package contains two command-line tools to convert whole-slide
images to and from DICOM. Support for proprietary file formats is
available through OpenSlide. The package also contains an Orthanc
plugin to display such DICOM images by any standard Web browser. The
implementation follows DICOM Supplement 145.
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pixelmed-apps
DICOM implementation containing Image Viewer and a ECG Viewer - cli
|
Versions of package pixelmed-apps |
Release | Version | Architectures |
bullseye | 20200416-4 | all |
jessie | 20140816-1 | all |
buster | 20150917+git20151209.36f3174+dfsg-1 | all |
stretch | 20150917-1 | all |
bookworm | 20220618+dfsg-1 | all |
sid | 20220618+dfsg-2 | all |
upstream | 20241027 |
|
License: DFSG free
|
This is a stand-alone DICOM toolkit that implements code for reading
and creating DICOM data, DICOM network and file support, a database of
DICOM objects, support for display of directories, images, reports and
spectra, and DICOM object validation.
Provide command line applications for using pixelmed
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plastimatch
medical image reconstruction and registration
|
Versions of package plastimatch |
Release | Version | Architectures |
sid | 1.9.4+dfsg.1-3 | amd64 |
trixie | 1.9.4+dfsg.1-3 | amd64 |
bookworm | 1.9.4+dfsg.1-1 | amd64 |
bullseye | 1.9.3+dfsg.1-1 | amd64,i386 |
buster | 1.7.4+dfsg.1-2 | amd64,i386 |
stretch | 1.6.5+dfsg.1-1 | amd64,i386 |
jessie | 1.5.16+dfsg-2 | amd64,armel,armhf,i386 |
upstream | 1.10.0 |
Debtags of package plastimatch: |
field | medicine:imaging |
role | program |
|
License: DFSG free
|
Plastimatch is an open source software for deformable image
registration. It is designed for high-performance volumetric
registration of medical images, such as X-ray computed tomography (CT),
magnetic resonance imaging (MRI), and positron emission tomography(PET).
Software features include:
- B-spline method for deformable image registration (GPU and multicore
accelerated), including support for image masking, landmark penalties,
and regularization
- Demons method for deformable image registration (GPU accelerated)
- Multi-atlas segmentation
- ITK-based algorithms for translation, rigid, affine, multiple demons
methods, and B-spline registration
- Pipelined, multi-stage registration framework with seamless conversion
between most algorithms and transform types
- Landmark-based deformable registration using thinplate splines for
global registration
- Landmark-based deformable registration using radial basis functions
for local corrections
- Broad support for 3D image file formats (using ITK), including DICOM,
Nifti, NRRD, MetaImage, and Analyze
-
Extensive toolchain for radiotherapy research, including support for
DICOM, DICOM-RT, DICOM SRO, XiO file format, gamma analysis, contour
manipulation, contour overlap analysis, and vector field analysis
Plastimatch also features two handy utilities which are not directly
related to image registration:
-
FDK cone-beam CT reconstruction (GPU and multicore accelerated)
- Digitally reconstructed radiograph (DRR) generation (GPU and multicore
accelerated)
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python3-dipy
Python library for the analysis of diffusion MRI datasets
|
Versions of package python3-dipy |
Release | Version | Architectures |
bookworm | 1.6.0-1 | all |
trixie | 1.10.0-1 | all |
sid | 1.10.0-2 | all |
bullseye | 1.3.0-3 | all |
|
License: DFSG free
|
DIPY is a software project for computational neuroanatomy. It focuses
on diffusion magnetic resonance imaging (dMRI) analysis and
tractography but also contains implementations of other computational
imaging methods such as denoising and registration that are
applicable to the greater medical imaging and image processing
communities. Additionally, DIPY is an international project which
brings together scientists across labs and countries to share their
state-of-the-art code and expertise in the same codebase,
accelerating scientific research in medical imaging.
Here are some of the highlights:
- Reconstruction algorithms: CSD, DSI, GQI, DTI, DKI, QBI, SHORE
and MAPMRI
- Fiber tracking algorithms: deterministic and probabilistic
- Native linear and nonlinear registration of images
- Fast operations on streamlines (selection, resampling, registration)
- Tractography segmentation and clustering
- Many image operations, e.g., reslicing or denoising with NLMEANS
- Estimation of distances/correspondences between streamlines and
connectivity matrices
- Interactive visualization of streamlines in the space of images
This package contains the Python 3 version.
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python3-nibabel
Python3 bindings to various neuroimaging data formats
|
Versions of package python3-nibabel |
Release | Version | Architectures |
bullseye | 3.2.1-2 | all |
buster | 2.3.2-1 | all |
trixie | 5.3.2-2 | all |
stretch | 2.1.0-1 | all |
sid | 5.3.2-2 | all |
bookworm | 5.0.0-2 | all |
|
License: DFSG free
|
NiBabel provides read and write access to some common medical and
neuroimaging file formats, including: ANALYZE (plain, SPM99, SPM2), GIFTI,
NIfTI1, MINC, as well as PAR/REC. The various image format classes give full
or selective access to header (meta) information and access to the image data
is made available via NumPy arrays. NiBabel is the successor of PyNIfTI.
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python3-nipy
Analysis of structural and functional neuroimaging data
|
Versions of package python3-nipy |
Release | Version | Architectures |
sid | 0.6.1-1 | all |
trixie | 0.6.1-1 | all |
bookworm | 0.5.0-7 | all |
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License: DFSG free
|
NiPy is a Python-based framework for the analysis of structural and
functional neuroimaging data. It provides functionality for
- General linear model (GLM) statistical analysis
- Combined slice time correction and motion correction
- General image registration routines with flexible cost functions,
optimizers and re-sampling schemes
- Image segmentation
- Basic visualization of results in 2D and 3D
- Basic time series diagnostics
- Clustering and activation pattern analysis across subjects
- Reproducibility analysis for group studies
Please cite:
K. Jarrod Millman and Matthew Brett:
Analysis of functional magnetic resonance imaging in Python
(eprint)
Computing in Science & Engineering
9(3):52-55
(2007)
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python3-nipype
Neuroimaging data analysis pipelines in Python3
|
Versions of package python3-nipype |
Release | Version | Architectures |
sid | 1.9.0-1 | all |
bullseye | 1.6.0-2 | all |
bookworm | 1.8.5-3 | all |
trixie | 1.9.0-1 | all |
upstream | 1.9.2 |
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License: DFSG free
|
Nipype interfaces Python to other neuroimaging packages and creates
an API for specifying a full analysis pipeline in Python. Currently,
it has interfaces for SPM, FSL, AFNI, Freesurfer, but could be
extended for other packages (such as lipsia).
Please cite:
SS Ghosh, C Burns, D Clark, K Gorgolewski, YO Halchenko, C Madison, R Tungaraza and KJ Millman:
Nipype: Opensource platform for unified and replicable interaction with existing neuroimaging tools
(eprint)
16th Annual Meeting of the Organization for Human Brain Mapping
:106
(2010)
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python3-nitime
timeseries analysis for neuroscience data (nitime)
|
Versions of package python3-nitime |
Release | Version | Architectures |
trixie | 0.11-3 | all |
bullseye | 0.9-1 | all |
sid | 0.11-3 | all |
bookworm | 0.9-5 | all |
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License: DFSG free
|
Nitime is a Python module for time-series analysis of data from
neuroscience experiments. It contains a core of numerical algorithms
for time-series analysis both in the time and spectral domains, a set
of container objects to represent time-series, and auxiliary objects
that expose a high level interface to the numerical machinery and
make common analysis tasks easy to express with compact and
semantically clear code.
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python3-pydicom
DICOM medical file reading and writing (Python 3)
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Versions of package python3-pydicom |
Release | Version | Architectures |
bookworm | 2.3.1-1 | all |
sid | 2.4.3-1 | all |
trixie | 2.4.3-1 | all |
buster | 1.2.1-1 | all |
bullseye | 2.0.0-1 | all |
upstream | 3.0.1 |
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License: DFSG free
|
pydicom is a pure Python module for parsing DICOM files. DICOM is a
standard (http://medical.nema.org) for communicating medical images
and related information such as reports and radiotherapy objects.
pydicom makes it easy to read DICOM files into natural pythonic
structures for easy manipulation. Modified datasets can be written
again to DICOM format files.
This package installs the module for Python 3.
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python3-pyxid
interface for Cedrus XID and StimTracker devices
|
Versions of package python3-pyxid |
Release | Version | Architectures |
trixie | 1.0-6 | all |
sid | 1.0-6 | all |
bookworm | 1.0-6 | all |
bullseye | 1.0-4 | all |
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License: DFSG free
|
pyxid is a Python library for interfacing with Cedrus XID (eXperiment
Interface Device) and StimTracker devices. XID devices are used in
software such as SuperLab, Presentation, and ePrime for receiving
input as part of stimulus/response testing experiments.
pyxid handles all of the low level device handling for XID devices in
Python projects.
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python3-surfer
visualize Freesurfer's data in Python3
|
Versions of package python3-surfer |
Release | Version | Architectures |
bookworm | 0.11.0-4 | all |
trixie | 0.11.2-1 | all |
sid | 0.11.2-1 | all |
bullseye | 0.11.0-1 | all |
|
License: DFSG free
|
This is a Python3 package for visualization and interaction with cortical
surface representations of neuroimaging data from Freesurfer. It
extends Mayavi’s powerful visualization engine with a high-level interface for
working with MRI and MEG data.
PySurfer offers both a command-line interface designed to broadly replicate
Freesurfer’s Tksurfer program as well as a Python library for writing scripts
to efficiently explore complex datasets.
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sightcalibrator
Camera calibration software
|
Versions of package sightcalibrator |
Release | Version | Architectures |
sid | 24.1.0-1 | amd64 |
trixie | 24.1.0-1 | amd64 |
bookworm | 21.1.1-3 | amd64 |
|
License: DFSG free
|
User-friendly application to calibrate mono and stereo cameras.
SightCalibrator can take images, video files, or any supported
camera device as input. It detects the presence of a checkerboard
in images. The parameters of the checkboard can be customized.
Individual images can then be marked to be used in the
computation of the calibration. Last, the intrinsic and extrinsic
parameters can be exported in OpenCV format, Yaml or XML.
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sightviewer
|
Versions of package sightviewer |
Release | Version | Architectures |
bookworm | 21.1.1-3 | amd64 |
trixie | 24.1.0-1 | amd64 |
sid | 24.1.0-1 | amd64 |
|
License: DFSG free
|
Medical image viewer featuring negatoscope, multi-planar
reconstruction, and volume rendering.
Many image formats are handled such as DICOM, mhd,
inr.gz, vtk, vti,... Reconstructions can also be imported from
DICOM segmentations or VTK supported formats, and visualized
in mixed rendering with images.
Tools are provided to measure distances of
structures in the image and to place landmarks.
Last, SightViewer can also connect directly to a PACS, and
then request, download or upload DICOM files.
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sigviewer
GUI viewer for biosignals such as EEG, EMG, and ECG
|
Versions of package sigviewer |
Release | Version | Architectures |
sid | 0.6.4-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 0.5.1+svn556-4 | amd64,armel,armhf,i386 |
stretch | 0.5.1+svn556-5 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 0.6.2-2 | amd64,arm64,armhf,i386 |
bullseye | 0.6.4-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 0.6.4-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 0.6.4-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package sigviewer: |
interface | x11 |
role | program |
uitoolkit | qt |
use | viewing |
x11 | application |
|
License: DFSG free
|
SigViewer is a viewing and scoring software for biomedical signal
data. It relies on biosig4c++ library which supports a number of
data formats (including EDF, BDF, GDF, BrainVision, BCI2000, CFWB,
HL7aECG, SCP_ECG (EN1064), MFER, ACQ, CNT(Neuroscan), DEMG, EGI,
EEG1100, FAMOS, SigmaPLpro, TMS32). The complete list of supported
file formats is available at
http://pub.ist.ac.at/~schloegl/biosig/TESTED .
Besides displaying biosignals, SigViewer supports creating
annotations to select artifacts or specific events.
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sofa-apps
GUI for the Simulation Open Framework Architecture (SOFA)
|
Versions of package sofa-apps |
Release | Version | Architectures |
buster | 1.0~beta4-12 | amd64,arm64,armhf,i386 |
stretch | 1.0~beta4-11 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.0~beta4-9 | amd64,armel,armhf,i386 |
Debtags of package sofa-apps: |
interface | x11 |
role | program |
uitoolkit | qt |
x11 | application |
|
License: DFSG free
|
SOFA is an Open Source framework primarily targeted at
real-time simulation, with an emphasis on medical simulation.
It is mostly intended for the research community to help
develop newer algorithms, but can also be used as an efficient
prototyping tool.
This package contains the SOFA main application.
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teem-apps
Tools to process and visualize scientific data and images - command line tools
|
Versions of package teem-apps |
Release | Version | Architectures |
sid | 1.12.0~20160122-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 1.11.0~svn6057-1.1 | amd64,armel,armhf,i386,mips,mipsel,s390x |
bullseye | 1.12.0~20160122-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.12.0~20160122-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 1.11.0~svn5226-1 | amd64,armel,armhf,i386 |
bookworm | 1.12.0~20160122-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package teem-apps: |
interface | commandline |
role | program |
|
License: DFSG free
|
Teem is a coordinated group of libraries for representing, processing, and
visualizing scientific raster data. Teem includes command-line tools that
permit the library functions to be quickly applied to files and streams,
without having to write any code. The most important and useful libraries in
Teem are:
- Nrrd (and the unu command-line tool on top of it) supports a range of
operations for transforming N-dimensional raster data (resample, crop,
slice, project, histogram, etc.), as well as the NRRD file format for
storing arrays and their meta-information.
- Gage: fast convolution-based measurements at arbitrary point locations in
volume datasets (scalar, vector, tensor, etc.)
- Mite: a multi-threaded ray-casting volume render with transfer functions
based on any quantity Gage can measure
- Ten: for estimating, processing, and visualizing diffusion tensor fields,
including fiber tractography methods.
This package contains some simple command-line tools which provide fast and
easy access to the functionality in the various libraries.
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tifffile
Read and write image data from and to TIFF files
|
Versions of package tifffile |
Release | Version | Architectures |
buster | 20181128-1+deb10u1 | amd64,arm64,armhf,i386 |
|
License: DFSG free
|
Image and meta-data can be read from TIFF, BigTIFF, OME-TIFF, STK, LSM, NIH,
ImageJ, MicroManager, FluoView, SEQ and GEL files.
Only a subset of the TIFF specification is supported, mainly uncompressed and
losslessly compressed 2**(0 to 6) bit integer, 16, 32 and 64-bit float,
grayscale and RGB(A) images, which are commonly used in bio-scientific imaging.
Specifically, reading JPEG/CCITT compressed image data or EXIF/IPTC/GPS/XMP
meta-data is not implemented. Only primary info records are read for STK,
FluoView, MicroManager, and NIH image formats.
TIFF, the Tagged Image File Format, is under the control of Adobe Systems.
BigTIFF allows for files greater than 4 GB. STK, LSM, FluoView, SEQ, GEL, and
OME-TIFF, are custom extensions defined by MetaMorph, Carl Zeiss MicroImaging,
Olympus, Media Cybernetics, Molecular Dynamics, and the Open Microscopy
Environment consortium respectively.
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voxbo
processing, statistical analysis, and display of brain imaging data
|
Versions of package voxbo |
Release | Version | Architectures |
buster | 1.8.5~svn1246-3 | amd64,arm64,armhf,i386 |
jessie | 1.8.5~svn1246-1.1 | amd64,armel,armhf,i386 |
stretch | 1.8.5~svn1246-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package voxbo: |
field | medicine:imaging |
role | program |
uitoolkit | qt |
|
License: DFSG free
|
This is a toolkit for analysis of functional neuroimaging (chiefly
fMRI) experiments and voxel-based lesion-behavior mapping. VoxBo
supports the modified GLM (for autocorrelated data), as well as the
standard GLM for non-autocorrelated data. The toolkit is designed to be
interoperable with AFNI, FSL, SPM and others.
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vrrender
|
Versions of package vrrender |
Release | Version | Architectures |
bullseye | 20.2.0-2 | amd64,i386 |
|
License: DFSG free
|
Medical image viewer featuring negatoscope, multi-planar
reconstruction, and volume rendering.
Many image formats are handled such as DICOM, mhd,
inr.gz, vtk, vti,... Segmentations meshes can also
be imported from DICOM and vtk formats, and visualized
in mixed rendering with images.
Tools are provided to measure distances of
structures in the image and to place landmarks.
Last, VRRender can also connect directly to a PACS, and
then request, download or upload DICOM files.
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vtk-dicom-tools
|
Versions of package vtk-dicom-tools |
Release | Version | Architectures |
sid | 0.8.14-3.1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
experimental | 0.8.14-3.2~exp1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 0.8.14-3.1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 0.8.12-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 0.8.9-1 | amd64,arm64,armhf,i386 |
stretch | 0.7.10-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 0.5.5-2 | amd64,armel,armhf,i386 |
upstream | 0.8.17 |
|
License: DFSG free
|
This package contains a set of classes for managing DICOM
files and metadata from within VTK, and some utility programs
for interrogating and converting DICOM files.
Command line tools
|
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xmedcon
Medical Image (DICOM, ECAT, ...) conversion tool (GUI)
|
Versions of package xmedcon |
Release | Version | Architectures |
trixie | 0.24.0-gtk3+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 0.23.0-gtk3+dfsg-1+deb12u1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 0.16.3+dfsg-1+deb11u1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 0.13.0-2 | amd64,armel,armhf,i386 |
buster | 0.16.1+dfsg-1 | amd64,arm64,armhf,i386 |
stretch | 0.14.1-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 0.24.0-gtk3+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
upstream | 0.24.1-gtk3 |
Debtags of package xmedcon: |
field | biology |
interface | commandline, x11 |
role | program |
scope | utility |
uitoolkit | gtk |
use | converting |
works-with | image, image:raster |
x11 | application |
|
License: DFSG free
|
This project stands for Medical Image Conversion. Released under the
(L)GPL, it comes with the full C-source code of the library, a
flexible command line utility and a neat graphical front-end using
the GTK+ toolkit. The currently supported formats are: Acr/Nema 2.0,
Analyze (SPM), DICOM 3.0, InterFile 3.3 and PNG.
The program also allows one to read unsupported files without
compression, to print pixel values or to extract/reorder specified
images. It is possible to retrieve the raw binary/ascii image arrays
or to write PNG for desktop applications.
This is the program version for X based on GTK+. Processes only one
file at a time.
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|
Official Debian packages with lower relevance
cmtk
Computational Morphometry Toolkit
|
Versions of package cmtk |
Release | Version | Architectures |
stretch | 3.3.1-1.1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 3.2.2-1.3 | amd64,armel,armhf,i386 |
buster | 3.3.1p1+dfsg-1 | amd64,arm64,armhf,i386 |
sid | 3.3.1p2+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 3.3.1p2+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 3.3.1p1+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
upstream | 3.4.0 |
|
License: DFSG free
|
A software toolkit for computational morphometry of biomedical
images, CMTK comprises a set of command line tools and a back-end
general-purpose library for processing and I/O.
The command line tools primarily provide the following functionality:
registration (affine and nonrigid; single and multi-channel; pairwise
and groupwise), image correction (MR bias field estimation;
interleaved image artifact correction), processing (filters;
combination of segmentations via voting and STAPLE; shape-based
averaging), statistics (t-tests; general linear regression).
|
|
connectomeviewer
Interactive Analysis and Visualization for MR Connectomics
|
Versions of package connectomeviewer |
Release | Version | Architectures |
buster | 2.1.0+dfsg-1 | all |
jessie | 2.1.0-1 | all |
|
License: DFSG free
|
The Connectome Viewer is a extensible, scriptable, pythonic research
environment for visualization and (network) analysis in neuroimaging
and connectomics.
Employing the Connectome File Format, diverse data types such as
networks, surfaces, volumes, tracks and metadata are handled and
integrated. The Connectome Viewer is part of the MR Connectome Toolkit.
|
|
elastix
toolbox for rigid and nonrigid registration of images
|
Versions of package elastix |
Release | Version | Architectures |
stretch | 4.8-10 | amd64,i386 |
bullseye | 4.9.0-2 | amd64,i386 |
buster | 4.9.0-1 | amd64,i386 |
sid | 5.1.0-1 | amd64 |
trixie | 5.1.0-1 | amd64 |
jessie | 4.7-2 | amd64,i386 |
bookworm | 5.0.1-4 | amd64 |
upstream | 5.2.0 |
Debtags of package elastix: |
role | program |
|
License: DFSG free
|
Image registration based on the well-known Insight Segmentation and
Registration Toolkit (ITK). The software consists of a collection of
algorithms that are commonly used to solve (medical) image
registration problems. The modular design of elastix allows the user
to quickly configure, test, and compare different registration
methods for a specific application. A command-line interface enables
automated processing of large numbers of data sets, by means of
scripting.
|
|
illustrate
cartoonish representations of large biological molecules
|
Versions of package illustrate |
Release | Version | Architectures |
trixie | 0.0+git20200923.217db48-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 0.0+git20200923.217db48-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 0.0+git20200923.217db48-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
upstream | 0.0+git20240817.e469df4 |
|
License: DFSG free
|
This package provides a binary to transform PDF-formatted proteins into
simplified but instructive graphics. The software has been used for
the Protein-of-the-month's biomolecular illustrations for the past 20
years.
|
|
imagemagick
??? missing short description for package imagemagick :-(
|
Versions of package imagemagick |
Release | Version | Architectures |
buster-security | 6.9.10.23+dfsg-2.1+deb10u7 | amd64,arm64,armhf,i386 |
bullseye-security | 6.9.11.60+dfsg-1.3+deb11u3 | amd64,arm64,armhf,i386 |
bullseye | 6.9.11.60+dfsg-1.3+deb11u4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm-security | 6.9.11.60+dfsg-1.6+deb12u1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 6.8.9.9-5+deb8u12 | amd64,armel,armhf,i386 |
jessie-security | 6.8.9.9-5+deb8u19 | amd64,armel,armhf,i386 |
stretch | 6.9.7.4+dfsg-11+deb9u8 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
stretch-security | 6.9.7.4+dfsg-11+deb9u13 | i386 |
stretch-security | 6.9.7.4+dfsg-11+deb9u14 | amd64,arm64,armel,armhf |
trixie | 7.1.1.39+dfsg1-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 6.9.10.23+dfsg-2.1+deb10u1 | amd64,arm64,armhf,i386 |
bookworm | 6.9.11.60+dfsg-1.6+deb12u2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 7.1.1.39+dfsg1-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
upstream | 7.1.1.42 |
Debtags of package imagemagick: |
interface | commandline, x11 |
role | program |
scope | utility |
uitoolkit | xlib |
use | converting, editing, viewing |
works-with | image, image:raster |
works-with-format | gif, jpg, pdf, png, postscript, svg, tiff |
x11 | application |
|
License: DFSG free
|
|
|
imview
Image viewing and analysis application
|
Versions of package imview |
Release | Version | Architectures |
bullseye | 1.1.9h-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 1.1.9c-12 | amd64,armel,armhf,i386 |
stretch | 1.1.9c-17 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.1.9h-1 | amd64,arm64,armhf,i386 |
bookworm | 1.1.9h-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.1.9h-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.1.9h-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package imview: |
role | program |
works-with | image, image:raster |
|
License: DFSG free
|
Imview is an application which
- Displays a large number of image formats.
- Displays 2D or 3D (as slices) images with a very good zoom and pan
feature.
- Works with multi-spectral, time series or multi-page documents (e.g.:
Satellite images, TIFF stacks, animated GIFs and heterogeneous
multi-component files).
- Displays all pixel types (1-bit to 64-bit data, integer or floating
point).
- Arbitrary 1-D profile of 2-D images (or of 2-D slices of 3-D images) can
be displayed.
- Has support for arbitrary colourmaps for all pixel types (i.e.: false
colour display).
- Has standard image manipulation facilities (brightness/contrast, gamma,
zoom, crop, rotation, etc).
- Can be controlled remotely via sockets and text commands (for easy
integration into various image analysis systems).
- Images can be uploaded into Imview via sockets or shared memory.
- And much more!
Please cite:
Hugues Talbot:
ImView: a portable image display application
(eprint)
|
|
orthanc-dicomweb
Plugin to extend Orthanc with support of WADO and DICOMweb
|
Versions of package orthanc-dicomweb |
Release | Version | Architectures |
bookworm | 1.7+dfsg-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 0.6+dfsg-1 | amd64,arm64,armhf,i386 |
trixie | 1.17+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 0.3+dfsg-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 1.18+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 1.5+dfsg-3 | amd64,arm64,armhf,i386,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
Orthanc DICOMweb is a plugin to Orthanc, the lightweight, RESTful Vendor
Neutral Archive for medical imaging. It extends the Orthanc core with
support of the WADO (now known as WADO-URI) and DICOMweb (QIDO-RS,
STOW-RS, WADO-RS) standards.
|
|
orthanc-gdcm
DICOM transcoder/decoder for Orthanc using GDCM (notably for JPEG2k)
|
Versions of package orthanc-gdcm |
Release | Version | Architectures |
bullseye | 1.2-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.5-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.8+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.8+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
|
License: DFSG free
|
This package installs a plugin for Orthanc, the lightweight, RESTful
Vendor Neutral Archive for medical imaging. The plugin extends
Orthanc with a transcoder/decoder of DICOM images that is built on
the GDCM library, whereas the built-in transcoder/decoder of Orthanc
uses DCMTK.
This plugin is notably necessary for Orthanc to be able to
transcode and decode JPEG2k transfer syntaxes.
|
|
orthanc-imagej
ImageJ plugin to import images from Orthanc
|
Versions of package orthanc-imagej |
Release | Version | Architectures |
stretch | 1.1+dfsg-1 | all |
bullseye | 1.2+dfsg-3 | all |
bookworm | 1.2+dfsg-3 | all |
trixie | 1.2+dfsg-4 | all |
buster | 1.2+dfsg-1 | all |
sid | 1.2+dfsg-4 | all |
|
License: DFSG free
|
This ImageJ plugin allows ImageJ to browse the content of an Orthanc
server, then import 2D/3D DICOM images from Orthanc into ImageJ.
Orthanc is a lightweight, RESTful DICOM server for healthcare and
medical research.
This plugin simplifies the indexation of DICOM images if using
ImageJ (e.g. for quality control of DICOM modalities, or for
pedagogical use). There is also no need to carry on any complex
network configuration, since the plugin directly uses the REST
API of Orthanc. This makes its installation and its use
quite straightforward.
|
|
orthanc-mysql
Plugins to use MySQL or MariaDB as a database back-end to Orthanc
|
Versions of package orthanc-mysql |
Release | Version | Architectures |
bullseye | 3.0-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 5.0+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 5.0+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 2.0-2 | amd64,arm64,armhf,i386 |
bookworm | 4.3-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
Orthanc MySQL is a set of two plugins to Orthanc, a lightweight,
RESTful Vendor Neutral Archive for medical imaging. These plugins
override the default SQLite engine of Orthanc with a MySQL or
MariaDB back-end. They bring scalability to Orthanc, making it
enterprise-ready.
|
|
orthanc-neuro
Neuroimaging plugin for Orthanc
|
Versions of package orthanc-neuro |
Release | Version | Architectures |
bookworm | 1.0-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1.1+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1.1+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
|
License: DFSG free
|
This package installs a plugin for Orthanc, the lightweight, RESTful
Vendor Neutral Archive for medical imaging. This plugin adds support
for neuroimaging in Orthanc, notably to easily convert from DICOM to
NIfTI.
|
|
orthanc-postgresql
Plugins to use PostgreSQL as a database back-end to Orthanc
|
Versions of package orthanc-postgresql |
Release | Version | Architectures |
stretch | 2.0-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bullseye | 3.3-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 5.0+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 5.0+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 4.0-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 3.2-1 | amd64,arm64,armhf,i386 |
upstream | 7.0 |
|
License: DFSG free
|
Orthanc PostgreSQL is a set of two plugins to Orthanc, a lightweight,
RESTful Vendor Neutral Archive for medical imaging. These plugins
override the default SQLite engine of Orthanc with a PostgreSQL
back-end. They bring scalability to Orthanc, making it
enterprise-ready.
|
|
orthanc-webviewer
Web viewer of medical images for Orthanc
|
Versions of package orthanc-webviewer |
Release | Version | Architectures |
trixie | 2.9+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 2.2-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 2.9+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 2.5-1 | amd64,arm64,armhf,i386 |
bullseye | 2.7-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 2.8-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
Orthanc Web Viewer is a plugin to Orthanc, a lightweight, RESTful Vendor
Neutral Archive for medical imaging. It extends Orthanc with an integrated
Web viewer of DICOM images.
|
|
paraview
Parallel Visualization Application
|
Versions of package paraview |
Release | Version | Architectures |
stretch | 5.1.2+dfsg1-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 5.12.1+dfsg-4 | ppc64el |
sid | 5.13.1+dfsg-9 | riscv64 |
sid | 5.13.1+dfsg-10 | amd64,arm64,i386,s390x |
buster | 5.4.1+dfsg4-3.1 | amd64,arm64,armhf,i386 |
bullseye | 5.9.0-2 | amd64,arm64,i386,mips64el,ppc64el,s390x |
bookworm | 5.11.0+dfsg-1 | amd64,arm64,i386,ppc64el,s390x |
jessie | 4.1.0+dfsg+1-1 | amd64,armel,armhf,i386 |
Debtags of package paraview: |
role | program |
uitoolkit | qt |
use | viewing |
|
License: DFSG free
|
ParaView is an open-source, multi-platform application designed to
visualize data sets of size varying from small to very large. The
goals of the ParaView project include the following:
* Develop an open-source, multi-platform visualization application.
* Support distributed computation models to process large data sets.
* Create an open, flexible, and intuitive user interface.
* Develop an extensible architecture based on open standards.
ParaView runs on distributed and shared memory parallel as well as
single processor systems and has been successfully tested on Windows,
Mac OS X, Linux and various Unix workstations, clusters and
supercomputers. Under the hood, ParaView uses the Visualization
Toolkit as the data processing and rendering engine and has a user
interface written using Qt.
|
|
pngquant
PNG (Portable Network Graphics) image optimising utility
|
Versions of package pngquant |
Release | Version | Architectures |
jessie | 2.3.0-1 | amd64,armel,armhf,i386 |
bullseye | 2.13.1-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 2.17.0-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 2.18.0-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 2.18.0-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 2.5.0-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 2.12.2-1 | amd64,arm64,armhf,i386 |
jessie-security | 2.3.0-1+deb8u1 | amd64,armel,armhf,i386 |
Debtags of package pngquant: |
interface | commandline |
role | program |
scope | utility |
use | compressing, converting |
works-with | image, image:raster |
works-with-format | png |
|
License: DFSG free
|
pngquant is a command-line conversion utility to quantize and dither truecolor
PNG images, especially those with a full alpha channel, down to 8-bit (or
smaller) RGBA-palette PNGs. Such images are usually two to four times smaller
than the full 32-bit versions, and partial transparency is preserved quite
nicely. This makes pngquant especially useful both for Web sites and for
PlayStation 2 development, where one of the texture formats is
RGBA-palette-based (though not PNG-compressed).
This is the same technique used for many of the images on the Miscellaneous
Transparent PNGs page (http://www.libpng.org/pub/png/pngs-img.html), and
the results are often indistinguishable from the original, truecolor PNG
images.
Optimizers (like pngcrush and optipng) optimize the compression, usually
losslessly, while pngquant quantizes colors down to 256 (or fewer) distinct
RGBA combinations, which is lossy.
|
|
science-workflow
workflow management systems useful for scientific research
|
Versions of package science-workflow |
Release | Version | Architectures |
bookworm | 1.14.5 | all |
stretch | 1.7 | all |
buster | 1.10 | all |
trixie | 1.14.7 | all |
sid | 1.14.7 | all |
bullseye | 1.14.2 | all |
|
License: DFSG free
|
This task lists some packages providing workflow management
systems useful for scientific research.
|
|
trimage
GUI and command-line interface to optimize image files
|
Versions of package trimage |
Release | Version | Architectures |
bookworm | 1.0.6-2 | all |
jessie | 1.0.5-1 | all |
stretch | 1.0.5-1.1 | all |
buster | 1.0.5+git20130126.e47888e-1 | all |
bullseye | 1.0.6-1 | all |
trixie | 1.0.6-2 | all |
sid | 1.0.6-2 | all |
Debtags of package trimage: |
interface | commandline, x11 |
role | program |
scope | utility |
uitoolkit | qt |
works-with | image |
works-with-format | jpg, png |
x11 | application |
|
License: DFSG free
|
Trimage is a cross-platform GUI and command-line interface to optimize image
files via optipng, advpng, pngcrush and jpegoptim, depending on the filetype
(currently, PNG and JPG files are supported). All image files are losslessly
compressed on the highest available compression levels. Trimage gives you
various input functions to fit your own workflow: A regular file dialog,
dragging and dropping and various command line options.
|
|
Debian packages in contrib or non-free
bart-cuda
tools for computational magnetic resonance imaging
|
Versions of package bart-cuda |
Release | Version | Architectures |
bullseye | 0.6.00-1+deb11u1 (contrib) | amd64 |
bookworm | 0.8.00-2 (contrib) | amd64 |
sid | 0.8.00-2 (contrib) | amd64 |
upstream | 0.9.00 |
|
License: DFSG free, but needs non-free components
|
The Berkeley Advanced Reconstruction Toolbox (BART) is a free and
open-source image-reconstruction framework for Computational Magnetic
Resonance Imaging. It consists of a programming library and a toolbox
of command-line programs. The library provides common operations on
multi-dimensional arrays, Fourier and wavelet transforms, as well as
generic implementations of iterative optimization algorithms. The
command-line tools provide direct access to basic operations on
multi-dimensional arrays as well as efficient implementations of
many calibration and reconstruction algorithms for parallel imaging,
compressed sensing, and machine learning.
This package provides BART with CUDA support.
|
fsl
transitional dummy package
|
Versions of package fsl |
Release | Version | Architectures |
buster | 5.0.8-6 (non-free) | all |
jessie | 5.0.7-4 (non-free) | all |
Debtags of package fsl: |
field | medicine:imaging |
interface | commandline, x11 |
role | program |
uitoolkit | tk |
use | analysing |
x11 | application |
|
License: non-free
|
The only purpose of this package is to enable upgrades to the new 'fsl-core'
package which replaces 'fsl'. This package can safely be removed.
Users aiming to perform a complete FSL installation (including all data
components) are advised to install the 'fsl-complete' package from
NeuroDebian.
Please cite:
Mark Jenkinson, Christian F. Beckmann, Timothy E. J. Behrens, Mark W. Woolrich and Stephen M. Smith:
FSL.
(PubMed)
NeuroImage
62(2):782-790
(2012)
|
vmtk
the Vascular Modeling Toolkit
|
Versions of package vmtk |
Release | Version | Architectures |
buster | 1.3+dfsg-2.3 (non-free) | all |
stretch | 1.3+dfsg-2.1+deb9u1 (non-free) | all |
jessie | 1.0.1-3 (non-free) | all |
|
License: non-free
|
The Vascular Modeling Toolkit is a collection of libraries and tools for
3D reconstruction, geometric analysis, mesh generation and surface data
analysis for image-based modeling of blood vessels.
|
Packaging has started and developers might try the packaging code in VCS
bioimagesuite
integrated image analysis software suite
|
Versions of package bioimagesuite |
Release | Version | Architectures |
VCS | 2.0-1 | all |
|
License: GPL-2+
Debian package not available
Version: 2.0-1
|
BioImage Suite has extensive capabilities for both neuro/cardiac
and abdominal image analysis and state of the art visualization.
Many packages are available that are highly extensible, and provide
functionality for image visualization and registration, surface
editing, cardiac 4D multi-slice editing, diffusion tensor image
processing, mouse segmentation and registration, and much more. It
can be integrated with other biomedical image processing software,
such as FSL and SPM. This site provides information, downloads,
documentation, and other resources for users of the software.
BioImage Suite was developed at Yale University and has been
extensively used at different labs at Yale since 2004.
|
bioimagexd
Analyzing, processing and visualizing of multi dimensional microscopy images
|
Versions of package bioimagexd |
Release | Version | Architectures |
VCS | 1.0-r1799-1 | all |
|
License: GPL-2
Debian package not available
Version: 1.0-r1799-1
|
BioImageXD is a multi-purpose post-processing tool for bioimaging. The
software can be used for simple visualization of multi-channel temporal image
stacks to complex 3D rendering of multiple channels at once. Animations of 3D
renderings can be created using flying paths or keyframes. BioImageXD has basic
image adjustment operations and a collection of noise reduction methods.
Processing methods are accompanied with a selection of segmentation methods.
Segmentation results can be analysed for tens of parameters or used for motion
tracking. Other quantitative analysis methods include for instance voxel and
object colocalization methods and internalization analysis. All processing and
analysis methods can be build into pipelines and run for hundreds of datasets
at once in batch processor.
|
cellprofiler
quantitatively measure phenotypes from images automatically
|
Versions of package cellprofiler |
Release | Version | Architectures |
VCS | 3.0.0-1 | all |
|
License: GPL-2
Debian package not available
Version: 3.0.0-1
|
CellProfiler is cell image analysis software designed to enable
biologists without training in computer vision or programming to
quantitatively measure phenotypes from thousands of images
automatically.
|
crea
base library of the creaTools medical image processing suite
|
Versions of package crea |
Release | Version | Architectures |
VCS | 0.0.20131107-1 | all |
|
License: CeCILL-B
Debian package not available
Version: 0.0.20131107-1
|
The CreaTools are a suite of medical image processing and visualization
software and development tools. They are developed by CREATIS, a
research unit with extensive experience in the medical image processing
field.
The CreaTools are a set of tools designed to meet both the needs of the
end-users (physicians, students or researchers) and of the developers.
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dicoogle
Java Advanced Imaging API reference implementation
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Versions of package dicoogle |
Release | Version | Architectures |
VCS | 2.5.0-1 | all |
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License: free
Debian package not available
Version: 2.5.0-1
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This project contains the source code for the core Java Advanced Imaging API
reference implementation containing the packages javax.media.jai. and
com.sun.media.jai..
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fiji
"batteries-included" distribution of ImageJ
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Versions of package fiji |
Release | Version | Architectures |
VCS | 2.3.1-1 | all |
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License: GPL-2 or GPL-3 or Public domain
Version: 2.3.1-1
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Fiji is an image processing package — a "batteries-included"
distribution of ImageJ, bundling many plugins which facilitate
scientific image analysis for the life sciences.
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freesurfer
analysis and visualization of functional brain imaging data
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Versions of package freesurfer |
Release | Version | Architectures |
VCS | 5.1.0+dev+cvs20120104-1 | all |
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License: FreeSurfer-Software-License-Agreement
Debian package not available
Version: 5.1.0+dev+cvs20120104-1
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FreeSurfer is a set of tools for analysis and visualization of
structural and functional brain imaging data. It contains a fully
automatic structural stream for processing cross sectional and
longitudinal data.
FreeSurfer provides many anatomical analysis tools, including:
representation of the cortical surface between white and gray matter,
representation of the pial surface, segmentation of white matter from
the rest of the brain, skull stripping, B1 bias field correction,
nonlinear registration of the cortical surface of an individual with
an sterotaxic atlas, labeling of regions of the cortical surface,
statistical analysis of group morphometry differences, and labeling of
subcortical brain structures, etc.
This package depends upon the latest version of freesurfer.
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incf-nidash-oneclick-clients
utility for pushing DICOM data to the INCF datasharing server
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License: BSD
Debian package not available
Language: Python
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A command line utility for anonymizing and sending DICOM data to the XNAT
image database at the International Neuroinformatics Coordinating Facility
(INCF). This tool is maintained by the INCF NeuroImaging DataSharing (NIDASH)
task force.
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insightapplications
InsightToolKit (ITK) based medical imaging applications
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Versions of package insightapplications |
Release | Version | Architectures |
VCS | 3.20.0-1.1 | all |
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License: BSD
Debian package not available
Version: 3.20.0-1.1
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A variety of applications providing segmentation, registration, and
other medical image processing algorithms such as MRI bias field
correction.
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jist
Java Image Science Toolkit
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Versions of package jist |
Release | Version | Architectures |
VCS | 2.0.20100907.dfsg1-1 | all |
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License: free
Debian package not available
Version: 2.0.20100907.dfsg1-1
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Java Image Science Toolkit (JIST) provides a native Java-based
imaging processing environment similar to the ITK/VTK
paradigm. Initially developed as an extension to MIPAV (CIT, NIH,
Bethesda, MD), the JIST processing infrastructure provides automated
GUI generation for application plug-ins, graphical layout tools, and
command line interfaces.
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kradview
medical image viewer for DICOM images
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Versions of package kradview |
Release | Version | Architectures |
VCS | 1.1.0-2 | all |
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License: GPL-3+
Debian package not available
Version: 1.1.0-2
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Kradview is a viewer of images obtained for some different sources: X-ray,
NMR and DICOM-compatible imaging devices. Its aim is a easy to use DICOM viewer
with instant rendering of images, no matter the size and the zoom of the DICOM
image. It covers the "let's see the the X-ray image" need of the medical
professional.
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libdcm4che-java
Clinical Image and Object Management
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Versions of package libdcm4che-java |
Release | Version | Architectures |
VCS | 5.10.6-1 | all |
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License: Apache-2.0 or LGPL-2
Debian package not available
Version: 5.10.6-1
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Dcm4che is a collection of open source applications and utilities for
the healthcare enterprise.
At the core of the dcm4che project is a robust implementation of the
DICOM standard. The dcm4che DICOM toolkit is used in many production
applications across the world.
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mayam
Cross-platform DICOM Viewer
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Versions of package mayam |
Release | Version | Architectures |
VCS | 0.8-1 | all |
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License: MPL 1.1/GPL 2.0/LGPL 2.1
Debian package not available
Version: 0.8-1
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A Cross-platform DICOM viewer using the dcm4che toolkit.
The current features are:
- DICOM Listener for Q/R
- DICOM Send
- Local DB for storing study information
- Importing DICOM studies from local disk
- Parsing DicomDir from local disk or CD
- Query compressed studies without decompressing them
- Multiple Studies viewer using Layout,Tab view
- Export to JPEG (Study, Series, Instance level). Windowing can be
applied to a single instance or series of instance while exporting
- Cine Loop & stack navigation
- Toggle for Text and Annotation Overlay
- Windowing Presets Settings (based on modality)
- Layout Settings (based on modality)
- AE Management
- DICOM Tags Viewer
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micromanager
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Versions of package micromanager |
Release | Version | Architectures |
VCS | 1.4.10-1 | all |
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License: free
Version: 1.4.10-1
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µManager is a software package for control of automated microscopes. It lets
you execute common microscope image acquisition strategies such as time-lapses,
multi-channel imaging, z-stacks, and combinations thereof. μManager works with
microscopes from all four major manufacturers (Leica, Nikon, Olympus and
Zeiss), most scientific-grade cameras and many peripherals (stages, filter
wheels, shutters, etc.) used in microscope imaging (check the list of supported
hardware). Since μManager runs as a plugin to ImageJ, image analysis routines
are available within the application.
Unencumbered code provides a GUI for microscope image acquisition, a hardware
interface layer and hardware interfacing for:
- ASI stages, filter wheels and shutters
- Arduino
- Conix filter changer
- Velleman K8055 and K8061 digital IO boards
- Leica DMI microscopes
- Ludl shutters, stages and filter Wheels
- Nikon TE2000 microscope
- Physik Instrumente stages
- Pecon stage incubators
- Prior shutters, stages and filter wheels
- Spectral LMM5 laser controller
- Sutter shutters, filter wheels and DG4
- Vincent Uniblitz shutters
- Yokogawa spinning disk confocal CSU22 and CSUX
- Zeiss microscopes (two 'generations')
- iidc1394 compatible cameras (through libdc1394)
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mipav
quantitative analysis and visualization of medical images
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Versions of package mipav |
Release | Version | Architectures |
VCS | 5.0.0.20100907-2 | all |
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License: non-free
Version: 5.0.0.20100907-2
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The MIPAV (Medical Image Processing, Analysis, and Visualization)
application enables quantitative analysis and visualization of
medical images of numerous modalities such as PET, MRI, CT, or
microscopy. Using MIPAV's standard user-interface and analysis
tools, researchers at remote sites can easily share research data and
analyses, thereby enhancing their ability to research, diagnose,
monitor, and treat medical disorders. MIPAV provides an interface
for plug-ins and serves as the foundation for other projects
(e.g. JIST).
This package provides downloader/installer for non-redistributable
closed-source version of MIPAV and a convenience startup wrapper.
You will have a choice of reviewing the license and accepting or
declining it upon installation.
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mni-colin27-nifti
Talairach stereotaxic space template
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Versions of package mni-colin27-nifti |
Release | Version | Architectures |
VCS | 1.1-2 | all |
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License: free
Version: 1.1-2
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This template MRI volume was created from 27 T1-weighted MRI scans of a
single individual that have been transformed into the Talairach stereotaxic
space. The anatomical image is complemented by a brain and a head mask.
All images are in 1x1x1 mm resolution.
This package provides the template in NIfTI format.
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openelectrophy
data analysis GUI for intra- and extra-cellular recordings
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Versions of package openelectrophy |
Release | Version | Architectures |
VCS | 0.0.svn143 | all |
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License: free
Version: 0.0.svn143
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This package provides the startup script for the OpenElectrophy GUI.
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openmeeg-tools
openmeeg library -- command line tools
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Versions of package openmeeg-tools |
Release | Version | Architectures |
VCS | 2.4.2-1 | all |
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License: CeCILL-B
Debian package not available
Version: 2.4.2-1
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OpenMEEG consists of state-of-the art solvers for forward problems in
the field of MEG and EEG. Solvers are based on the symmetric
Boundary Element method [Kybic et al, 2005], providing excellent
accuracy, particularly for superficial cortical sources. OpenMEEG can
compute four types of lead fields (EEG, MEG, Internal Potential and
Electrical Impedence Tomography).
This package provides command line interface to openmeeg functionality.
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slicer
software package for visualization and image analysis - main application
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Versions of package slicer |
Release | Version | Architectures |
VCS | 4.10.2-1 | all |
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License: free
Debian package not available
Version: 4.10.2-1
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Slicer is an application for computer scientists and clinical researchers. The
platform provides functionality for segmentation, registration and
three-dimensional visualization of multi-modal image data, as well as advanced
image analysis algorithms for diffusion tensor imaging, functional magnetic
resonance imaging and image-guided therapy. Standard image file formats are
supported, and the application integrates interface capabilities to biomedical
research software and image informatics frameworks.
3D Slicer main application.
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stabilitycalc
evaluate fMRI scanner stability
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License: BSD
Language: Python
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Command-line tools to calculate numerous fMRI scanner stability metrics, based
on the FBIRN quality assurance test protocal. Any 4D volumetric timeseries
image in NIfTI format is support input. Output is a rich HTML report.
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tools for volumetric image analysis
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Versions of package via-bin |
Release | Version | Architectures |
VCS | 1.6.0-3.1 | all |
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License: free
Version: 1.6.0-3.1
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VIA is a volumetric image analysis suite for functional and structural
(medical) images. The suite consists of different tools ranging from
simple data handling over viewers to complex image transformation.
All tools operate on data in VISTA format. The package contains several
converters from e.g. PNG, PGM or PNM to this data format and back.
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interactive parallel visualization and graphical analysis tool
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Versions of package visit |
Release | Version | Architectures |
VCS | 2.9.1-1 | all |
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License: free
Debian package not available
Version: 2.9.1-1
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VisIt is a free interactive parallel visualization and graphical
analysis tool for viewing scientific data. Users can quickly generate
visualizations from their data, animate them through time, manipulate
them, and save the resulting images for presentations. VisIt contains
a rich set of visualization features so that you can view your data in
a variety of ways. It can be used to visualize scalar and vector
fields defined on two- and three-dimensional (2D and 3D) structured and
unstructured meshes.
VisIt was designed to handle very large data set sizes in the terascale
range and yet can also handle small data sets in the kilobyte range.
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xnat
platform for data management and productivity tasks in neuroimaging
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Versions of package xnat |
Release | Version | Architectures |
VCS | 1.7.5.1-1 | all |
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License: XNAT_SLA
Debian package not available
Version: 1.7.5.1-1
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The primary functionality of XNAT is to provide a place to store and
control access to neuroimaging data. This includes sophisticated user
control, search and retrieval, and archiving capabilities. As
open-source software, XNAT also supports a wide variety of
research-based processing pipelines, and is able to link up with
supercomputer processing power to dramatically shorten image
processing time.
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Unofficial packages built by somebody else
cdmedicpacs
web interface to PACS to access DICOM study images
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License: GPL2
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Web based PACS (Picture Archiving and Communication System) to access DICOM
studies images, in an easy and quick manner.
- Easy configuration of PACS nodes (AE,IP,Port) , status, statistics
of storage form web interface.
- Dynamic web page generation from DICOM data +- prospective preparation
when system is idle.
- Automatic video(mp4/gif) generation from Heart MRI at Patient’s heart
bit frame rate and XA at 15 fps.
- Still images in jpeg with Window/Level from DICOM header when present
or with Histogram algorithm.
- Possibility on large Studies of still images to make a single mp4 for
Series instead of a bunch of jpeg.
- Easy web deletion of Series/Studies and auto deletion (Study date/DB
insertion) for temporal PACS.
- Good DICOM interaction with Diagnostic Modalities and commercial DICOM
Viewers/Work Stations.
- Good DICOM interaction with free DICOM Viewers Aeskulap
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mni-autoreg
MNI average brain (305 MRI) stereotaxic registration model
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License: no-free, but GPLed parts
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This package provides a version of the MNI Average Brain (an average of 305
T1-weighted MRI scans, linearly transformed to Talairach space) specially
adapted for use with the MNI Linear Registration Package.
- average_305.mnc - a version of the average MRI that covers the whole brain
(unlike the original Talairach atlas), sampled with 1mm cubic voxels
- average_305_mask.mnc - a mask of the brain in average_305.mnc
- average_305_headmask.mnc - another mask, required for nonlinear mode
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mni-n3
MNI Non-parametric Non-uniformity Normalization
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License: BSDish
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MNI Non-parametric Non-uniformity Normalization (N3). This package provides
the 'nu_correct' tool for unsupervised correction of radio frequency (RF)
field inhomogenities in MR volumes. Two packages are provided:
- mni-n3 - provides 'nu_correct'
- libebtks-dev - MNI support library with numerical types and algorithms
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opendicom.net
API to DICOM in C# for Mono
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License: LGPL
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The openDICOM.NET project implements a new approach towards DICOM
(Digital Imaging and Communications in Medicine) libraries. DICOM is
a worldwide standard in Medical IT and is provided by the National
Electrical Manufacturers Association (NEMA). This standard specifies
the way medical images and meta data like study or patient related
data is stored and communicated over different digital medias. Thus,
DICOM is a binary protocol and data format.
The openDICOM# Class Library, main part of the openDICOM.NET project,
provides an API to DICOM in C# for Mono and the .NET Framework. It is
a completely new implementation of DICOM. In contrast to other
similar libraries the intention of this implementation is to provide
a clean classification with support of unidirectional DICOM data
streaming. Another implemented goal is the support of DICOM as
XML. This is not standard conform but very use- and powerful within
software development, storage and manipulation. Currently, full read
support of DICOM output stream and full write support to XML is
supposed to be provided. The entire DICOM content can be accessed as
sequence or as tree of class instances. Latter is the default
representation of DICOM content by the library.
The openDICOM.NET Utils are a collection of console tools for working
with the needed data dictionaries in different data formats (binary
and textual), query of ACR-NEMA (prior DICOM standard) and DICOM
files and transcoding them into image formats like JPEG and XML
files. These utils are written in C# for Mono and the .NET Framework
and are using the openDICOM# API for processing.
The openDICOM.NET Navigator recapitulates the openDICOM.NET Utils in
form of a GTK# GUI. It provides different views with focus on DICOM
data sets and visualization. Connectivity to GIMP is also given for
single image processing purpose as well as the possibility to run
through multi-frame images like a movie.
The openDICOM.NET Beagle Filter Plugin increases the usability of
ACR-NEMA and DICOM query within your desktop. It makes DICOM content
overall indexable for retrieval. The Beagle search engine relies on
Mono/.NET and works in the background of your system, but is able to
detect content changes in realtime (depending on your configuration).
All GUI applications focus the popular GNOME desktop, but are 100%
platform independent by relying on Mono.
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No known packages available but some record of interest (WNPP bug)
Delft Visualization and Image processing Development Environment
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License: BSD
Debian package not available
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DeVIDE, or the Delft Visualization and Image processing Development
Environment, is a Python-based dataflow application builder that enables
the rapid prototyping of medical visualization and image processing
applications via visual programming. In other words, by visually connecting
functional blocks (think Yahoo pipes), you can create cool visualizations.
See the DeVIDE website at http://visualisation.tudelft.nl/Projects/DeVIDE
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DTI spatial normalization and atlas construction toolkit
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License: GPL-3+
Debian package not available
Language: C++
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DTI-TK is a spatial normalization & atlas construction toolkit,
designed from ground up to support the manipulation of
diffusion-tensor images (DTI) with special cares taken to respect the
tensorial nature of the data. It implements a state-of-the-art
registration algorithm that drives the alignment of white matter (WM)
tracts by matching the orientation of the underlying fiber bundle at
each voxel. The algorithm has been shown to both improve WM tract
alignment and to enhance the power of statistical inference in
clinical settings. The key features include:
- NIfTI support for scalar, vector and DTI volumes
- tool chains for manipulating DTI volumes: resampling, smoothing,
warping, registration & visualization
- pipelines for WM morphometry: spatial normalization & atlas
construction for population-based studies
- built-in cluster-computing support
- interoperability with other major DTI tools: AFNI, Camino,
DTIStudio & FSL
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toolbox for processing and visualization of electrophysiological data
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License: GPL-2+
Debian package not available
Language: C, Matlab/Octave
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EEGLAB is an interactive Matlab toolbox for processing continuous and
event-related EEG, MEG and other electrophysiological data
incorporating independent component analysis (ICA), time/frequency
analysis, artifact rejection, event-related statistics, and several
useful modes of visualization of the averaged and single-trial data.
Please register by following this link if you are using eeglab.
Please cite:
Delorme A and Makeig S:
EEGLAB: an open source toolbox for analysis of single-trial EEG dynamics
(2004)
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I/O framework for neuroimaging data
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License: GPL-2+
Debian package not available
Language: C++
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This framework aids access of and conversion between various established
neuro-imaging data formats, like Nifti, Analyze, DICOM and VISTA. ISIS
is extensible with plugins to add support for additional data formats.
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high performance computing MRI simulator
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License: GPL-2+
Debian package not available
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JEMRIS, which stands for "Juelich Extensible MRI Simulator", is
a general simulator of MRI (Magnetic Resonance Imaging) data.
The general process of simulation consists of preparation by choice or
implementation of sequence, sample and coil setup and the invocation
of the simulation run itself.
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medical image referral, archiving, routing and viewing system
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License: GPL
Debian package not available
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OpenSourcePACS is a free, open source image referral, archiving,
routing and viewing system. It adds functionality beyond conventional
PACS by integrating wet read functions, implemented through DICOM
Presentation State and Structured Reporting standards.
In its first release, OpenSourcePACS delivers a complete wet read
system, enabling an imaging clinic or hospital to offer its services
over the web to physicians within or outside the institution. In
future releases, we hope to incorporate more RIS (dictation,
transcription, and reporting) functionality.
OpenSourcePACS is a product of the UCLA Medical Imaging Informatics
group (http://www.mii.ucla.edu/).
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No known packages available
blox
medical imaging and visualization program
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License: GPL
Debian package not available
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The purpose of the project is to develop a quantitative medical
imaging and visualization program for use on brain MR, DTI and MRS
data. It is a joint project of the Kennedy Krieger Institute and the
Johns Hopkins University, Psychiatric Neuroimaging Lab
(http://pni.med.jhu.edu/methods/morph.htm).
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brainvisa
image processing factory for MR images
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License: Free? (CeCill License)
Debian package not available
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BrainVISA is a software, which embodies an image processing
factory. A simple control panel allows the user to trigger some
sequences of treatments on series of images. These treatments are
performed by calls to command lines provided by different
laboratories. These command lines, hence, are the building blocks on
which are built the assembly lines of the factory. BrainVISA is
distributed with a toolbox of building blocks dedicated to the
segmentation of T1-weighted MR images. The product of the main
assembly line made up from this toolbox is the following: grey/white
classification for Voxel Based Morphometry, Meshes of each hemisphere
surface for visualization purpose, Spherical meshes of each
hemisphere white matter surface, a graph of the cortical folds, a
labeling of the cortical folds according to a nomenclature of the
main sulci.
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dcm4chee
Clinical Image and Object Management (enterprise)
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License: LGPL, MPL, Apache, other (also non-free)
Debian package not available
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Contained within the dcm4che project is dcm4chee (the extra 'e'
stands for 'enterprise'). dcm4chee is an Image Manager/Image Archive
(according to IHE). The application contains the DICOM, HL7 services
and interfaces that are required to provide storage, retrieval, and
workflow to a healthcare environment. dcm4chee is pre-packaged and
deployed within the JBoss application server. By taking advantage of
many JBoss features (JMS, EJB, Servlet Engine, etc.), and assuming the
role of several IHE actors for the sake of interoperability, the
application provides many robust and scalable services.
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dicom4j
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License: GPL
Debian package not available
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Java framework for Dicom
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drjekyll
interactive voxel editor for viewing and editing three-dimensional images
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License: GPL
Debian package not available
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It is specifically aimed at postprocessing of segmented datasets,
but offers some functionality for raw data as well.
Voxel elements (=voxels) and pixel ("picture element") are viewed
as data sets and can be processed by this program as kind of
a final polishing process.
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dti-query
dynamic queries of the white matter brain pathways
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License: MIT
Debian package not available
Language: C++
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This application allows neuroscientists to place and interactively manipulate
box-shaped regions (or volumes of interest) to selectively display pathways
that pass through specific anatomical areas. A simple and extensible query
language allows for arbitrary combinations of these queries using Boolean
logic operators. Queries can be further restricted by numerical path
properties such as length, mean fractional anisotropy, and mean curvature.
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ecg2png
convert scanned electrocardiograms into PNG format
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License: GPL
Debian package not available
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This program is designed to convert scanned 12-lead
electrocardiograms into PNG format and a web-friendly image size. It
assumes that the electrocardiogram (ECG) is printed with a black line
on white paper with a red grid.
The problems this program is designed to solve are (1) an ECG scanned
at relatively high resolution (300 to 600 dots per inch) imposes a
substantial load on the web browser because it contains about 6
million pixels which may require 18 to 24 MB of RAM to store for
display. Also, (2) typical scanners convert a clean paper ECG into a
multitude of colors, include green and blue. The resulting file
cannot be compressed efficiently because it does not contain as much
redundancy, and thus takes more time to transmit over low-speed
network connections.
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gimias
Graphical Interface for Medical Image Analysis and Simulation
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License: BSD-like
Debian package not available
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GIMIAS is a workflow-oriented environment for solving advanced
biomedical image computing and individualized simulation problems, which
is extensible through the development of problem-specific plug-ins. In
addition, GIMIAS provides an open source framework for efficient
development of research and clinical software prototypes integrating
contributions from the Physiome community while allowing
business-friendly technology transfer and commercial product
development.
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hid
database management system for clinical imaging
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License: BSD, BIRN
Debian package not available
Language: java
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The Human Imaging Database (HID) is an extensible database management
system developed to handle the increasingly large and diverse
datasets collected as part of the MBIRN and FBIRN collaboratories and
throughout clinical imaging communities at large.
Please register by following this link if you are using hid.
Please cite:
Keator, D.B.; Grethe, J.S.; Marcus, D.; Ozyurt, B.;
Gadde, S.; Murphy, S.; Pieper, S.; Greve, D.;Notestine, R.; Bockholt,
H.J.; Papadopoulos, P.:
A National Human Neuroimaging Collaboratory Enabled
By The Biomedical Informatics Research Network (BIRN)
(2008)
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maris
package suite for Radiological Workflow
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License: GPL
Debian package not available
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The MARiS Project goal is to realize a package suite for Radiological
Workflow using Open Source tools and technologies in according with
IHE guidelines. The architecture of the single packages is based on
the concept of IHE actor: this is very useful to develop a system
that is an ensemble of single pieces that cooperate together using
IHE profiles.
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medisnap
photograph, manage, view, compare, document and archive medical photos
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License: GPL-3
Debian package not available
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Photograph, manage, view, compare, document and archive medical photos fully integrated
into doctor's practice systems. Take a photo and immediately see how the picture gets
archived to your current patient automatically.
- direct support for Olympus E-System cameras
- network support
- fully integrated via GDT interface into many medical software systems
- organise photos by patients effectively
- define your own localisations
- compare photos of healing processes at different times
- work time-optimized and effective, photos automatically get added and archived under
the current patient in your system
- easily print selected photos and archive or give them to your patients
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mesa-test-tools
IHE Test Software for Radiology
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License: free
Debian package not available
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The MESA software release which is available at
http://ihedoc.wustl.edu/mesasoftware/10.15.0/dist/ provides several
tools that might cover a wide range of applications for
Integrating the Healthcare Enterprise (IHE) testing.
Another important element of the IHE testing process is the set of
software tools HIMSS and RSNA have commissioned. Developed by the
Electronic Radiology Laboratory at the Mallinckrodt Institute of
Radiology, Washington University of St. Louis, the MESA tools are
designed for use by participating companies in implementing IHE
capabilities in their systems and preparing for the Connectathon. Their
purpose is to provide communication partners, test data and test plans
to allow organizations to provide a baseline level of testing as they
implement the IHE Technical Framework. These tools are made available to
participants during the period of an IHE demonstration year and are then
released into the public domain at the end of that cycle. The latest
version of the MESA Test Tools available in the public domain can be
found here.
This kind of software is definitively valuable for information systems
vendors and imaging systems vendors.
Because the CTN Debian package is based on an upstream dead project
these tools should have a high priority for packaging because the
CTN homepage http://erl.wustl.edu/research/dicom/ctn.html says:
"The CTN software is also embedded within the MESA tools. The version
of CTN software in those tools does not have a separate release number
but is more current than version 3.0.6."
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miview
Medical Images viewer and converter
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License: GPL-3+
Debian package not available
Language: C++
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MIView features
- DICOM files browser
- volume rendering
- reads DICOM v3, NEMA/ACR, Papyrus, Jpeg, GIF, bitmap, TIFF,
Analyze 7.5, and Nifti1 files
- can convert to raster (jpeg, bitmap, etc) and Analyze/Nifti1
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mni-icbm152-nlin-2009
MNI stereotaxic space human brain template
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License: custom, DFSG-compliant
Debian package not available
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This is an unbiased standard magnetic resonance imaging template volume for
the normal human population. It has been created by the Montreal Neurological
Institute (MNI) using anatomical data from the International Consortium for
Brain Mapping (ICBM).
The package provides a 1x1x1 mm and 0.5x0.5x0.5 mm resolution templates
(hemissphere-symetric and asymetric non-linearily co-registered versions),
some including T1w, T2w, PDw modalities, T2 relaxometry, and tissue probability
maps. In addition, it contains a lobe atlas, and masks for brain, eyes and
face.
Please cite:
V.S. Fonov, A.C. Evans, R.C. McKinstry, C.R. Almli and D.L. Collins:
Unbiased nonlinear average age-appropriate brain templates from birth to adulthood.
(2009)
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mrisim
simulator for magnetic resonance imaging data
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License: BSD-like
Debian package not available
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mrisim is a simple Magnetic Resonance Imaging (MRI) simulation program
which produces MINC volumes from a segmented and labelled brain phantom.
It allows intrinsic tissue parameters (T1, T2...) and pulse sequence
parameters (TR, TE ...) to be specified and then produces simulated
images with noise. Currently, no artifacts are implemented.
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omero
coming standard LIMS for microscopy images
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License: GPL
Debian package not available
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OMERO is client-server software for visualisation, management and
analysis of biological microscope images.
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piano
medical image processing library for surgical planning
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License: BSD
Debian package not available
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Piano is a library containing roughly 75 algorithms and tools for
multi-dimensional medical image processing, analysis and visualization.
It is used in the field of surgical planning.
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pymeg
suite for analysis of magnetoencephalography (MEG) data
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License: GPL-3
Debian package not available
Language: Python
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PyMEG is a project in Python to do various neuroimaging processing
with magnetoencephalography (MEG) data. The purpose of this project,
is to create a suite of functions to do MEG analysis in Python.
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stir
Software for Tomographic Image Reconstruction
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License: GPL
Debian package not available
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STIR is Open Source software for use in tomographic imaging. Its aim is to
provide a Multi-Platform Object-Oriented framework for all data manipulations
in tomographic imaging. Currently, the emphasis is on (iterative) image
reconstruction in PET, but other application areas and imaging modalities
can and might be added.
STIR is the successor of the PARAPET software library which was the result
of a (European Union funded) collaboration between 6 different partners,
the PARAPET project..
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tempo
3D visualization of brain electrical activity
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License: BSD
Debian package not available
Language: C++, Qt
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TEMPO is open source software for 3D visualization of brain electrical
activity. TEMPO accepts EEG file in standard EDF format and creates
animated sequence of topographic maps. Topographic maps are generated
over 3D head model and user is able to navigate around head and examine
maps from different viewpoints. Most mapping parameters are adjustable
through appropriate graphical user interface controls. Also, individual
topographic maps could be saved in PNG format for future examination or
publishing.
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