Debian Med Imaging packages

AMIDE: (Amide's a Medical Imaging Data Examiner) AMIDE は医用画像データセットの表示および分析用ツールです。各種ファイル フォーマットからインポートされた複数のデータセットの同時処理、画像統合、 関心のある三次元領域の描画や分析、ボリュームレンダリング、そして剛体ア ラインメントの機能が含まれます。

Amide は (DCMTK ライブラリを用いて) ほとんどの臨床 DICOM ファイルをイン ポートします。

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.

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.

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.

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

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.

DICOM はイメージ保存、アノテーション、ネットワーキングの標準規格です。これ は医療用画像で広く使われています。Central Test Node (CTN) は、この標準の実 装です。

このパッケージには、CTN のバイナリとランタイムコンフィグファイルが含まれて います。

CTSim は対話的なコンピュータ断層撮影シミュレータを提供します。コンピュータ 断層撮影は物体を透過する X 線の吸収量を計測して、その物体の内部を推定する技 法です。

CTSim にはコマンドラインツールとグラフィカルユーザインターフェースの両方が あります。CTSim には非常に教育的な追跡モードがあり、データ収集シミュレー ションと再構成を見ることができます。

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.

DCMTK には、DICOM 画像ファイルの調査や構築、変換、オフラインメディアの 操作、ネットワーク接続越しの画像の送受信、デモ用画像の保存、ワークリス トサーバなどに使うライブラリとアプリケーション集が含まれています。

本パッケージには DCMTK ユーティリティアプリケーションが含まれています。

注意: 本バージョンは libssl サポート付きでコンパイルされました。

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.

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.

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).

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.

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.

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.

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 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).

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

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.

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

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.

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.

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.

2Dおよび3Dグレイスケール画像に関する汎用画像処理タスクと三角メッシュに関する 基本的操作を行うためのコマンドラインツールです。サポートされる画像処理 アルゴリズムは画像フィルタリング、組み合わせ、画像レジストレーション、 一連の画像に対する運動補正、および複数の画像についての様々な統計量の推定です。 このパッケージにはこれらのコマンドラインツールへの nipype インターフェース も含まれます。

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.

本パッケージには、MINC ファイル操作用ツールが含まれます。

Minc ファイルフォーマットは、柔軟性が高い医用画像ファイルフォーマット であり、NetCDF 汎用データフォーマットを基盤にしています。 このフォーマットは、シンプルで、自己完結しており、拡張性が高く、 移植性が高く、多次元をサポートしており、プログラミングインターフェイスは 低レベルのデータアクセスと高レベルのボリューム操作の両方をサポートしています。 そしてこのライブラリを使った汎用の画像ファイル操作ツール集が用意されています。 フォーマット、ライブラリとツールは、医用画像研究環境での利用を想定して設計 されています。それゆえ、これらはシンプルかつパワフルであり、ユーザにきれい な外見を提供しようとしてはいません。

このパッケージは GUI ベースの (機能的) 核磁気共鳴画像法のための可視化および 解析ツールです。 MRIcron は脳解剖画像上での 2D および 3D の統計的オーバーレ イマップ描画の作成に使用できます。さらに、(刺激前後の信号の変化のプロットを 作成するなどの) 基本的な機能的時系列の分析だけでなく、解剖学的関心領域や病 変マッピングの描画を手助けします。

このパッケージは mricron に加え、DICOM および PAR/REC フォーマットの画像を NIfTI フォーマットに変換する dcm2nii とノンパラメトリック法によるデータ解析 を行う npm を含んでいます。

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.

Niftilib は、NIfTI-1 データフォーマットのファイルを読み書きするための I/O ライブラリです。NIfTI-1 とは、医学画像データ、すなわち、磁気共鳴画像 (MRI) や、functional MRI (fMRI) 脳画像のためのバイナリファイルフォーマットです。

本パッケージは、ライブラリに同梱されているツール群 (nifti_tool, nifti_stats および nifti1_test) を提供します。

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.

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.

OpenSlide はスライド全体画像、別名仮想スライドを読み込むシンプルなインター フェースを提供する C ライブラリです。

スライド全体画像、別名仮想スライドは、デジタル病理学で用いられる高解像度の 大きな画像です。これらの画像を、画像を解凍した状態で RAM もしくはスワップに 配置する、標準的な画像ツールおよびライブラリで読み込むのは困難です。全体ス ライド画像は日常的に RAM サイズを超過し、解凍状態では数十ギガバイト達しま す。加えて、全体スライド画像は概して複数解像度で、ある解像度では少量の画像 データしか必要ではありません。

このライブラリは現状で以下のフォーマットをサポートします。

• Aperio (.svs, .tif)
• Hamamatsu (.vms, .vmu, .ndpi)
• Leica (.scn)
• MIRAX (.mrxs)
• Sakura (.svslide)
• Trestle (.tif)
• Generic tiled TIFF (.tif)

本パッケージにはファイル操作用のコマンドラインツールが含まれます。

Orthanc は単純かつ強力な医療画像用 DICOM サーバを提供することを目標と しています。Orthanc は Windows または Linux を実行しているどんなコンピュータ をも Vendor Neutral Archive (換言すれば mini-PACS システム) に変えることが できます。アーキテクチャは軽量で、複雑なデータベース管理は必要なく、 サードパーティ依存パッケージをインストールする必要もありません。

Orthanc のユニークな点は、REST フルな API を提供する点です。この主要な 特徴のために、Orthanc はどんなコンピュータ言語からも駆動することができます。 格納された医療画像の DICOM タグは JSON ファイルフォーマットでダウンロード することができます。さらに、標準的 PNG 画像を DICOM インスタンスから オンザフライで生成することができます。

Orthanc により、ユーザは DICOM ファイルの内容に集中することができ、 DICOM フォーマットおよび DICOM プロトコルの複雑さは忘れることができます。

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.

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

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)

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.

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.

NiPy は脳構造画像解析および脳機能画像解析のための Python ベースのフレーム ワークです。次の機能を提供します。

• 一般線形モデル (GLM) 統計解析
• 混合スライスタイム補正と動き補正
• 柔軟なコスト関数、オプティマイザ、リサンプリングスキームを備える 汎用画像登録ルーティン
• 画像のセグメント化
• 結果の基礎的な 2D または 3D 可視化
• 基礎的な時系列診断
• 被写体間のクラスタリング解析および活性化パターン解析
• グループ研究用の再現性解析

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).

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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).

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.

有名な Insight Segmentation and Registration Toolkit (ITK) に基づく画像登録。 このソフトウェアは、(医学的な) 画像登録の問題を解決 するために一般的に使用される一連のアルゴリズムで構成されています。 elastix のモジュール式設計により、特定のアプリケーションのさまざまな 登録方法の構成、テスト、比較を高速に行うことができます。 コマンドラインインターフェイスにより、スクリプトを使用して大量の データセットを自動で処理することができます。

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.

Imview は次の機能を持つアプリケーションです。

• 多種多様な画像フォーマットを表示。
• 二次元または (スライスとして) 三次元画像を表示。(非常に便利なズーム およびパン機能付き)
• 多スペクトラム、時系列、又は複数ページの文書 (例: 衛星画像、TIFF スタック、 アニメーション GIF や多要素の混在するファイル) の処理。
• すべてのピクセルタイプ (1 ビットから 64 ビットデータ、整数又は浮動小数点) を表示。
• 二次元画像の任意の一次元プロファイル (または三次元画像の二次元スライス) を表示可能。
• 全ピクセルタイプに対して任意の色マップをサポート (即ち偽色表示)。
• 標準的な画像操作機能 (輝度/コントラスト調整、ガンマ補正、ズーム、切り取り、 回転など) をサポート。
• (各種画像分析システムへの統合を容易にするために) ソケットやテキストコマンド 経由で遠隔操作可能。
• その他いろいろ!

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.

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.

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 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.

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 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 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 は、小規模なものから非常に大規模なものまで様々なサイズの データセットを可視化するためのオープンソースかつ マルチプラットフォームなアプリケーションです。 ParaView プロジェクトの目標は以下に挙げたものを含みます。

* オープンソースでマルチプラットフォームな
  可視化アプリケーションを開発すること。
* 巨大なデータセットを処理するための分散計算モデルを
  サポートすること。
* オープンで柔軟、かつ直感的な
  ユーザーインターフェースを作成すること。
* オープンな標準に基づいた、拡張可能なアーキテクチャを開発すること。

ParaView は並列および単一プロセッサのシステムの 分散・共有されたメモリ上で実行できます。 また、Windows や Mac OS X、Linux や様々な Unix の ワークステーションやクラスタ、スーパーコンピュータで うまくテストされています。 内部的には、ParaView はデータ処理のためとレンダリングエンジンとして Visualization Toolkit を使っています。 また、Qt を使って書かれたユーザーインターフェースです。

pngquant は PNG 画像の量子化とディザリングのためのコマンドライン変換ユーティ リティで、特に truecolor PNG 画像でフルアルファチャンネルを持つものを 8 ビット (又はそれ以下) の RGBA パレット PNG 画像に変換するのに向いています。そのよう な画像は通常フル 32 ビット版に比べ 1/2 から 1/4 のサイズに縮小され、部分的な 透過度は十分に保持されます。この機能により、ウェブサイトと、テキスチャフォー マットが (PNG 圧縮ではない) RGBA パレットベースの PlayStation 2 での開発の 両方に、pngquant は特に役立ちます。 これは Miscellaneous Transparent PNG ページ (http://www.libpng.org/pub/png/pngs-img.html) の画像の多くで用いられているのと 同じ技術であり、その結果はオリジナルの truecolor PNG 画像とほとんど区別でき ません。

(pngcrush や optipng のような) 最適化ツールは、通常無損失で圧縮率を最適化し ます。 一方 pngquant は、色数を 256色 (又はそれ以下)の 別個の RGBA の組み合わせに量子化する、損失のある最適化を行います。

This task lists some packages providing workflow management systems useful for scientific research.

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.

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.