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.

BioSig 라이브러리에 기반한, 이 패키지는 아래 명령행 도구를 제공합니다.

• save2gdf: SCP-ECG(EN1064), HL7aECG (FDA-XML), GDF, EDF, BDF, CWFB를 포함하지만 이에 국한되지 않고 다양한 파일 형식간 변환.
• biosig2gdf: biosig 데이타 파일을 GDF로 변환하여 스크립팅 언어 (예. loadgdf.{py,r})로 구문 분석 및 로딩을 단순화
• rec2bin, bin2rec, heka2itx, save2aecg, save2scp: save2gdf 기반한 여러 변환 도구
• biosig_fhir: 생체 신호 데이타를 HL7/FFHIR 바이너리 템플릿 파일로 패킹
• physicalunits: ISO 11073-10101에 따른 물리적 유닛의 인코딩 및 디코딩 변환기

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 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.

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.

DCMTK에는 DICOM 이미지 파일 검사, 구성, 변환, 오프라인 미디어 처리, 네트워크 연결을 통한 이미지 송수신을 위한 라이브러리와 응용프로그램 모음 그리고 시연 이미지 저장장치와 작업목록 서버가 포함되어 있습니다.

이 패키지에는 DCMTK 유틸리티 응용프로그램을 포함합니다.

알림: 이 버전은 libssl 지원을 포함합니다.

DICOM 속성 파일을 생성, 수정, 덤프, 검증하기 위한 명령행 유틸리티. 일부 독점 의료 의미지 형식을 DICOM으로 변환 할 수 있습니다. 오래된 ACR/NEMA 형식 데이타와 SPI 같은 일부 독점 버젼을 처리할 수 있습니다.

DICOMscope는 모든 형식에 비압축, 단색 DICOM 이미지를 표시할 수 있으며, DICOM 파트 14 및 프리젠테이션 상태에 따라 모니터 보정을 지원하는 자유 DICOM 뷰어입니다.

DICOMscope는 부가적으로 Presentations LUT SOP Class를 구현하는 인쇄 클라이 언트(DICOM Basic Grayscale Print Management)를 제공합니다.

이 프로토타입 개발은 "COmmitte for the Advancement of DICOM"에 의해 위임 받 아 유럽 방사선 의학회 ECR 1999에서 시연되었습니다. 향상된 버젼은 RSNA InfoRAD 1999에 "DICOM Display Consistency Demonstration"을 위해 개발되었습니다.

현재 릴리즈는 ECR 2001에서 시연되었으며 인쇄 서버, 암호 DICOM 통신 지원, 디지털 서명, 구조화된 리포트등 여러 확장 기능을 포함합니다.

GDF (General Datafromat for Biosignals / 생체신호를 위한 일반 데이타형식)은 EEG, ECG, MEG 같은 생체신호를 위한 일반 저장소를 제공하기 위함입니다.

이 패키지는 라이브러리(gdf_merger)와 함께 포함되어 있는 도구를 제공합니다.

Ginkgo CADx는 고급 기능의 완벽한 DICOM 뷰어 솔류션을 제공하고 확장 기능을 지원합니다.

• 프로파일을 통한 쉽고 사용자 정의가 가능한 인터페이스.
• 완전한 기능을 갖춘 DICOM 이미지 시각화.
• 완벽한 도구 세트 (측정, 마커, 텍스트,...).
• 다중 기법 지원 (신경학, 방사선학, 피부학, 안과학, 초음파, 내시경 검사,...)
• JPEG, PNG, GIF, TIFF의 Dicomization 지원.
• 완전한 EMH 통합 지원: HL7 표준 및 IHE 준수 워크플로우.
• PACS 워크스테이션 (C-FIND, C-MOVE, C-STORE..)
• 사용자 지정 확장을 통한 확장 가능.
• 망막 이미지 모자이크 구성.
• 자동 망막 분석 진단.
• 건선 자동 진단.

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.

SNAP은 활성 외곽선 방법을 사용하여 의료 영상 (예. 뇌의 자기 공영 영상)에서 구조의 반자동 세분화와 수동 묘사 및 이미지 탐색을 제공합니다. 주목할만한 기 능은 아래와 같습니다:

• 원활한 3D 탐색을 위한 링크드 커서
• 한번에 3개의 직교 평면에서 수동 분할
• NIfTI를 포함한, 다양한 3D 이미지 형식 지원
• 여러 이미지의 동시, 링크드 뷰 및 분할 지원
• 컬러 이미지에 대한 제한된 지원 (예. 확산 텐서 맵)
• 분할 결과의 빠른 후처리를 위한 3D cut-plane 도구

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.

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.

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 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.

OpenSlide는 가상 슬라이더로 알려진 whole-slide 이미지를 읽기 위한 간단한 인터페이스를 제공하는 C 라이브러리입니다.

가상 슬라이더로 알려진 Whole-slide 이미지는 디지탈 병리학에서 사용되는 크고, 고해상도를 제공하는 이미지입니다. 이러한 도구들은 일반적으로 RAM 또는 스왑 파일에서 편하게 쉽게 압축을 해제할 수 있는 이미지를 위해 설계되었기 때문에 표준 이미지 도구 또는 라이브러리를 사용해서 이러한 이미지를 읽는 것은 어려운 일입니다. Whole-slide 이미지는 일상적으로 RAM 크기를 초과하며 압축을 해제시 종종 수십 기가를 차지하기도 합니다. 또한 whole-slide 이미지는 보통 다중 해상도를 가지며 특정 해상도에서는 소량의 이미지 데이타만 필요할 수도 있습니다.

이 라이브러리는 현재 다음을 지원합니다:

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

이 패키지는 파일 조작을 위한 명령행 도구를 포함합니다.

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

Plastimatch는 변형 이미지 등록을 위한 오픈 소스 소프트웨어입니다. 이는 X- ray 단층 촬영 (CT), 자기 공명 영상 (MRI), 양전자 방사 단층 촬영 (PET)과 같 은 의학 영상의 고성능 체적 등록을 위해 설계되었습니다. 이 소프트웨어는 아래 기능들을 포함합니다.

• 이미지 마스킹, 랜드 마크 페널티 및 정규화에 대한 지원을 포함하는, 변형 이미지 등록 (GPU 및 멀티 코어 가속)을 위한 B-spline 방법
• 변형 이미지 등록을 위한 데몬 방법 (GPU 가속)
• 멀티 아틀라스 분할
• 번역, 엄격함, 아핀, 멀티 데몬 방법 및 B-spline 등록을 위한 ITK 기반 알고리즘
• 대부분의 알고리즘 및 변환 유형간의 원활한 전환을 갖는 파이프라인, 다단계 등록 프레임워크
• 글로벌 등록을 위해 thinplate spline을 사용하는 랜드마크 기반 변형 등록
• 로컬 수정을 위해 방사형 기본 함수를 사용하는 랜드마크 기반 변형 등록
• DICOM, Nifti, NRRD, MetaImage, Anlyze를 포함하는 3D 이미지 파일 형식 (ITK 사용)을 위한 폭 넓은 지원

• DICOM, DICOM-RT, DICOM SRO, XiO 파일 형식, 감마 분석, 형상 조작, 형상 중첩 분석, 그리고 벡터 필드 분석을 위한 지원을 포함하는, 방사선 치료 연구를 위한 광범위한 툴체인 Plastimatch는 또한 이미지 등록과는 직접적으로 관련이 없지만 두개의 편리한 유틸리티를 제공합니다:

• FDK 콘 빔 CT 재구성 (GPU 및 멀티코어 가속)

• 디지탈 복원 방사선 (DRR) 발생 (GPU 및 멀티코어 가속)

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 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.

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.

SOFA는 의료 시뮬레이션에 중점을 둔, 주로 실시간 시뮬레이션을 목표로하는 오 픈 소스 프레임워크입니다. 주된 목적은 연구 커뮤니티가 새로운 알고리즘을 개 발할 수 있도록 도와주는 것 이지만, 효과적인 프로토타입 도구로도 사용될 수 있습니다.

이 패키지는 SOFA 주요 어플리케이션을 포함합니다.

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.

잘 알려진 Insight Segmentation and Registration Toolkit (ITK)를 기반으로 하는 이미지 등록. 이 소프트웨어는 (의료) 이미지 등록 문제를 해결하는데 일반적으로 사용되는 알고리즘 모음으로 구성됩니다. elastix의 모듈식 설계를 통해 사용자는 특정 애플리케이션에 대한 다양한 등록 방법을 신속하게 구성, 테스트 비교할 수 있습니다. 명령행 인터페이스는 대량의 데이타 세트를 스크립팅을 통해 자동으로 처리할 수 있도록 합니다.

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.

Imview는 아래의 특징들을 갖는 어플리케이션입니다.

• 다수의 이미지 형식 출력.
• 매우 훌륭한 줌 및 팬 기능을 가지고 2D 또는 3D (슬라이스로) 이미지를 를 출력.
• 다중 스펙트럼, 시간열 또는 다중 페이지 문서(예, 위성 영상, TIFF 스택, 애니메이트 GIF, 이기종 다중 구성 파일들)에서 작동합니다.
• 모든 픽셀 타입 출력 (1 비트에서 64비트 데이타, 정수 또는 부동 소수점).
• 2-D 이미지 (또는 3-D 이미지의 2-D 슬라이스)의 임의 1-D 프로필을 표시할 수 있습니다.
• 모든 픽셀 유형에 대해 임의의 컬러맵을 지원 (예: false colour display)
• 표준 이미지 조작 기능 (밝기/대비, 감마, 확대, 자르기, 회전등).
• 소켓과 텍스트 명령을 통해 리모트로 제어할 수 있습니다 (다양한 이미지 분석 시스템과 쉽게 통합 될 수 있습니다).
• 이미지는 소켓 또는 공유 메모리를 통해서 Imview에 업로드 될 수 있습니다.
• 그외에도 많은 것들이 있습니다!

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.

ParaView는 크기가 작은것 부터 매우 큰 것까지 매우 다양한 데이타 세트를 시각 화하도록 설계된 오픈소스, 멀티 플랫폼 어플리케이션입니다. ParaView 프로젝트 의 목적은 다음과 같습니다.

• 오픈소스, 멀티 플랫폼 시각화 어플리케이션 개발.
• 대형 데이타 세트 처리를 위한 분산 계산 모델 지원.
• 개방적이며, 유연하고, 직관적인 사용자 인터페이스 생성
• 오픈 표준을 기반으로 확장가능한 아키텍쳐 개발.

ParaView는 분산 및 공유 메모리의 병렬 및 싱글 프로세스 시스템에서 실행되며, Windows, Mac OS X, Linux 그리고 여러 유닉스 워크스테이션, 클러스터 및 슈퍼 컴퓨터에서 성공적으로 테스트가 완료되었습니다. 내부를 보면, ParaView는 데이 타 프로세싱 및 렌더링 엔진으로 시각화 툴킷을 사용하며, Qt를 사용해서 개발된 사용자 인터페이스를 가지고 있습니다.

pngquant는 양자화를 하는 명령행 변환 유틸리티로, 디더 트루 컬러 PNG 이미지, 특히 완전한 알파 채널을 가지고 있는 트루 컬러 PNG 이미지를 8-bit (또는 그 이하) RGBA-팔레트 PNG 파일로 다운합니다. 이렇게 변환된 이미지는 완전한 32-bit 버전보다 2에서 4배가량 작습니다, 그리고 특히 부분 투명성이 잘 보존됩 니다. 이는 pngquant를 특히 텍스쳐 형식에 하나가 RGBA-팔레트 기반 (PNG- compressed가 아니긴 하지만)인 웹 사이트 및 플레이스테이션 2 개발 모두에서 유용하도록 합니다. 이는 Miscellaneous Transparent PNG 페이지 (http://www.libpng.org/pub/png /pngs-img.html)에 있는 많은 이미지에서 사용되는 동일한 기술이며, 그 결과 원 래 트루컬러 PNG 이미지와 종종 구별이 되지 않습니다.

pngquant가 내용에 손실을 가져오는, 별개의 RGBA를 256 (또는 더 낮게)으로 색 상을 낮게 양자화하는 동안, (pngcrush 및 optipng 처럼) Optimizer 는 일반적으 로 무손실 방법으로 압축을 최적화 합니다.

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.

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.