Debian Med Imaging packages

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).

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 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.

CTSim впроваджує інтерактивну симуляцію комп’ютерного томографа. Комп’ютерна томографія дозволяє отримати уяву про внутрішню будову об’єкта по вимірюванню ступеня поглинання x-променів, що проходять крізь об’єкт.

CTSim має як графічний інтерфейс так і можливість керування з командного рядка. CTSim має дуже добрий навчальний режим для перегляду даних отриманих в ході симуляції, а також для реконструкції.

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 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.

Утиліти командного рядка для створення, зміни, вивантаження та перевірки файлів з DICOM-атрибутами. Підтримується перетворення деяких пропрієтарних форматів в DICOM. Можлива робота з більш старим форматом даних ACR/NEMA та деякими пропрієтарними версіями цього формату, такими як 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 надає можливість напівавтоматичної сегментації структур в медичних зображеннях (наприклад, магнітно-резонансних зображеннях мозку) за допомогою методу активних контурів, а також ручного розмежування та навігації по зображенню. Слід відзначити такі можливості:

• прив’язка курсору для плавної 3D-навігації;
• ручна сегментація одночасно в трьох ортогональних проекціях;
• підтримка різних форматів 3D-зображень, включаючи NIfTI;
• одночасний перегляд й сегментація декількох зображень;
• обмежена підтримка кольорових зображень (наприклад, карти тензора дифузії);
• інструмент обрізки 3D-проекції для прискорення подальшої обробки результатів сегментації.

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.

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.

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.

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.

Інструмент з графічним інтерфейсом для візуалізації та аналізу (Функціональної) магнітно-резонансної томографії. MRIcron може бути використаний для створення 2D і 3D візуалізацій статистичних накладних мап анатомічних зображень мозку. Крім того, він допомагає у промальовуванні анатомічних „областей інтересу“ (ROI), або відображенні ушкоджень, а також базового аналізу функціональних часових послідовностей (таймсерій) (наприклад, створення графіків зміни сигналу перистимулів).

На додаток до „mricron“ пакунок містить утиліту „dcm2nii“, яка підтримує перетворення зображень DICOM та PAR/REC у формат NIfTI, а також утиліту „npm“ для непараметричного аналізу даних.

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 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).

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 — це інфраструктура для магнітно-резонансної томографії (МРТ). Вона охоплює весь набір інструментів МРТ, від низькорівневого збору даних до реконструкції зображення. Зокрема, він спрямований на швидке прототипування послідовності даних МРТ. Послідовності можуть бути запрограмовані за допомогою високорівневого об’єктно-орієнтованого інтерфейсу програмування мовою Сі++. Надаються розширені інструменти аналізу послідовності даних, такі як інтерактивна побудова графіків траєкторій k-простору, користувацький інтерфейс для швидкого циклу компіляції, компонування, тестів, випробувань, а також має потужний МРТ-симулятор, який підтримує різні віртуальні зразки. Для швидкої і гнучкої реконструкції зображення, ODIN містить налаштовувану, багатопотокову інфраструктуру обробки даних.

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.

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.

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 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

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 — це модуль на Python для аналізу часових рядів даних з експериментів по неврології. Він містить ядро чисельних алгоритмів для аналізу часових рядів, як у часових так і у спектральних областях, набір об’єктів-контейнерів для подання часових рядів, а також допоміжні об’єкти, які надають інтерфейс високого рівня для чисельних машин та полегшення виконання задач загального аналізу поряд з компактним та семантично ясним кодом.

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.

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.

Це інструмент для аналізу даних, отриманих у функціональних нейровізуалізаційних експериментах (головним чином ФМРТ), та аналізу просторових зв’язків патологій. VoxBo підтримує модифіковані узагальнені лінійні моделі (GLM) для автокорельованих даних, окрім стандартних. Є можливість обміну даними з AFNI, FSL, SPM та іншими інструментами.

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.

Реєстрація зображень на основі добре відомого набору інструментів Insight Segmentation and Registration Toolkit (ITK). Програмне забезпечення являє собою набір алгоритмів, які зазвичай використовуються (в медицині) для вирішення проблеми реєстрації зображень. Модульна конструкція Elastix дозволяє користувачеві швидко налаштовувати, перевіряти й порівнювати різні методи реєстрації для конкретного застосунка. Інтерфейс командного рядка дозволяє автоматизувати за допомогою сценаріїв обробку великої кількості наборів даних.

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 це програма, яка:

• Працює з великою кількістю графічних форматів.
• Показує дво- та тривимірні (у проекціях) зображення з гарними можливостями збільшення та панорамування.
• Працює з багато-спектральними, багатосторінковими документами (наприклад: супутникові знімки поверхні, стеки TIFF, анімовані GIF та гетерогенні багато-компонентні файли).
• Показує всі типи пікселів (від 1-бітових до 64-бітових, цілі або з плаваючою точкою).
• Довільні одновимірні профілі двовимірних зображень (або двовимірні проекції тривимірних зображень) можуть бути показані.
• Підтримка довільних кольорових схем для всіх типів пікселів (наприклад: помилкові кольори дисплея).
• Має стандартні засоби для роботи із зображеннями (яскравість, контрастність, гамма, масштабування, кадрування, обертання, і т.д.).
• Може керуватись віддалено через сокети та текстові команди (для легкої інтеграції в різні системи аналізу зображень).
• Зображення можуть бути завантажені в Imview через сокети або розподіляєму пам'ять.
• Та багато іншого!

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 — багатоплатформний застосунок з відкритими джерельними кодами, розроблений для візуалізації наборів даних як великих розмірів так і малих. Метою проекту ParaView є:

• розробка застосунку для візуалізації, багатоплатформного з відкритими джерельними кодами

• підтримка розподіленої моделі обчислень, що оперують великими обсягами даних

• створення відкритого, гнучкого та інтуїтивно зрозумілого інтерфейсу користувача

• розробка гнучкої архітектури на основі відкритих стандартів

ParaView працює на системах із розділюваною та спільною пам’яттю, а також на однопроцесорних системах, її також було успішно протестовано у Windows, Linux, MacOS та різних робочих станціях Unix, а також кластерах й суперкомп’ютерах. ParaView використовує Visualization Toolkit в якості рушія для обробки та візуалізації даних; інтерфейс користувача написаний з використанням бібліотеки Qt.

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.

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

Trimage — мультиплатформовий графічний інтерфейс та інтерфейс командного рядка для оптимізації графічних файлів через optipng, advpng, pngcrush та jpegoptim, в залежності від типу файлу (на даний час підтримуються файли PNG й JPG). Усі файли зображень стискуються без втрат самим високим рівнем стиснення. Trimage надає різноманітні можливості вводу для відповідності з Вашим робочим процесом: звичайний файловий діалог, „перетягнення й кидання“ та різноманітні параметри командного рядка.

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.

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.

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.