Debian Med Imaging Development packages

Die CImg-Bibliothek ist ein C++-Toolkit, das einfache Klassen und Funktionen zum Laden, Speichern, Bearbeiten und Anzeigen von Bildern für den eigenen C++-Code bereitstellt. Das Paket besteht nur aus einer einzigen Header-Datei, die in den eigenen Quellcode eingebunden werden muss. CImg enthält nützliche Bildbearbeitungsalgorithmen zum Laden/Speichern, Skalieren/Rotieren, Filtern, Zeichnen (von Text, Linien, Flächen, Ellipsen, ...), usw.

Bilder werden von einer Klasse repräsentiert, die bis zu 4 Dimensionen (von eindimensionalen, skalaren Signalen bis zu Volumen aus vektorwertigen Pixeln) und »template pixel types« unterstützt. Die Bibliothek hat nur minimale Abhängigkeiten von anderen Bibliotheken: Sie kann schon mit den Standard-C-Bibliotheken kompiliert werden und. Sie erfordert keine exotischen Bibliotheken und komplexe Abhängigkeiten.

DICOM ist der Standard für die Speicherung, Kommentierung und den Austausch von Bildern. Es wird sehr oft für medizinische Bildverarbeitung benutzt.

Dieses Paket enthält die Headerdateien und die statische Bibliothek zur Erzeugung von Programmen, die die CTN-Bibliothek benutzen.

G'MIC is an open and full-featured framework for image processing, providing several different user interfaces to convert/manipulate/filter/visualize generic image datasets, from 1d scalar signals to 3d+t sequences of multi-spectral volumetric images.

This package contains the stand-alone gmic binary.

The Berkeley Advanced Reconstruction Toolbox (BART) is a free and open-source image-reconstruction framework for Computational Magnetic Resonance Imaging.

This package provides headers and static libraries.

BioSig is a library for accessing files in several biomedical 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 .

This package provides header files and static library.

Hilft Forscherinnen und Klinikärztinnen einfach und schnell zusammenzuarbeiten, um Anwendungen für computerassistierte Chirurgie zu entwickeln und zu testen, die medizinische Bildgebung, chirurgische Navigation und biomechanische Simulationen ermöglichen.

Dieses Paket enthält notwendige Entwicklungsdateien für den Bau von CamiTK-Anwendungen. Außerdem stellt das Paket für die Erstellung neuer Erweiterungen den CamiTK-Assistenten bereit.

CIFTI (Connectivity Informatics Technology Initiative) standardizes the file formats for storage of connectivity data. These formats are developed by the Human Connectome Project and other interested parties.

CiftiLib is a C++ library for CIFTI-1 and CIFTI-2 file I/O, supporting both on-disk and in-memory access. It also provides facilities for reading and writing generic NIfTI-1 and NIfTI-2 files.

This package provides the development files.

EDFlib is a programming library for C/C++ to read/write EDF+/BDF+ files. (It also reads old-type EDF/BDF files.) EDF means European Data Format. BDF is the 24-bits version of EDF.

Headers and shared libraries for edflib.

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.

Headers and static libraries for libgdcm. These are not needed to use GDCM, but are needed to build plugins or programs that link against libgdcm.

GDF (General Dataformat for Biosignals) is intended to provide a generic storage for biosignals, such as EEG, ECG, MEG etc.

This package provides the header files.

GIFTI is an XML-based file format for cortical surface data. This reference IO implementation is developed by the Neuroimaging Informatics Technology Initiative (NIfTI).

This package provides the header files and static library.

ITK ist ein quelloffener Werkzeugsatz zur Durchführung von Erkennung (»registration«) und Segmentierung (»segmentation«). Erkennung ist die Aufgabe der Ausrichtung von (und des Findens von Entsprechungen zwischen) Datensätzen. Segmentierung ist der Prozess der Identifizierung und Klassifizierung von digital repräsentierten Daten. Normalerweise stammen die Daten von medizinischen Geräten wie Computertomographen und Magnetresonanztomographen. Beispielsweise kann - im medizinischen Kontext - eine Computertomographie mit einer Magnetresonanztomographie ausgerichtet werden, um die in beiden Datensätzen enthaltene Information zu kombinieren.

Dieses Paket enthält die Entwicklungsdateien, mit denen Sie Ihre eigenen ITK-Anwendungen erstellen können.

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 development files.

This library implements an efficient minimum cut/maximum flow algorithms on graphs that can be used for exact or approximate energy minimization in low-level vision. The algorithm provides a high performance that makes near real-time performance possible. This package provides the development files for the library.

libmia comprises a set of libraries and plug-ins for general purpose 2D and 3D gray scale image processing and basic handling of triangular meshes. The libraries provide a basic infrastructure and generic algorithms, that can be specialized by specifying the appropriate plug-ins. This package provides the development files for the library.

This library implements handling for landmarks and 3D view positioning for optimal landmark visibility, and in-and output of these landmarks. This library is part of the MIA tool chain for medical image analysis. This package contains the development files - headers, shared libraries, and pkg-config files.

This package contains the library and headers for libminc2 and libminc_io.

The Minc file format is a highly flexible medical image file format. Minc version 1 is built on top of the NetCDF generalized data format. Minc version 2 is built on top of the HDF data format. This library handles both formats. In each case 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.

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 header files and static libraries of libnifti2.

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 development files.

Dieses Metapaket stellt die erforderlichen Entwicklungspakete für die Entwicklung von OpenCV (Open Computer Vision) zur Verfügung.

Die Open Computer Vision Library ist eine Algorithmensammlung und Beispielcode für verschiedene Aufgaben des maschinellen Sehens. Die Bibliothek ist mit IPL (Intels Image Processing Library) kompatibel und kann, falls verfügbar, IPP (Intels Integrated Performance Primitives) zur Leistungssteigerung verwenden.

OpenCV enthält maschinennahe portable Datentypen und Operatoren sowie einen Satz an High-Level-Funktionalitäten für Videoerfassung, Bildverarbeitung und -analyse, Strukturanalyse, Bewegungsanalyse und -verfolgung, Objekterkennung, Kamerakalibrierung und 3D-Rekonstruktion.

Open IGT Link is a simple network protocol intended for trackers, robots and other devices to send data to the main application. Some devices might also accept commands.

For example applications may include:

• Stereotactic surgical guidance using optical position sensor and medical image visualization software.
• Intraoperative image guidance using real-time MRI and medical image visualization software
• Robot-assisted intervention using robotic device and surgical planning software

This package contains the development files needed to build your own IGT applications.

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 development files needed to build OpenSlide applications.

PAPYRUS 3.0 file format based on the new DICOM 3.0 Standard addresses the open interchange of medical images in files or on removable storage media. This specific implementation of the DICOM standard is intended as a generic solution for interchange of multi-modality medical images on removable media. It can also be used for convenient exchange of image data between different computer systems through industry standard file transfer mechanisms. Finally it can also be used for storage and archival of medical image data in a DICOM compatible format.

This package contains the libraries needed to run PAPYRUS 3.0 applications.

The Surgical Image Guidance and Healthcare Toolkit aims to ease the creation of applications based on medical imaging. It includes various features such as 2D and 3D digital image processing, visualization, augmented reality and medical interaction simulation. It runs on many different environments (Windows, Linux, macOS), is written in C++, and features rapid interface design using XML files.

Sight was formerly known as FW4SPL. It was renamed in 2018, firstly to make its purpose clearer, and secondly as part of a major change in design and in the governance of the development team.

This package contains the development files.

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 provides the Teem header files required to compile C++ programs that use Teem to do 3D visualisation.

Vision with Generic Algorithms (VIGRA) is a computer vision library that puts its main emphasis on flexible algorithms, because algorithms represent the principle know-how of this field. The library was consequently built using generic programming as introduced by Stepanov and Musser and exemplified in the C++ Standard Template Library. By writing a few adapters (image iterators and accessors) you can use VIGRA's algorithms on top of your data structures, within your environment.

This package contains the header and development files needed to build programs and packages using VIGRA.

Vistaio is a library that handles loading and storing of data in a cross-platform manner. Its virtue is that the otherwise binary files provide an ascii header that makes it easy to get information about the contens of a file. It supports a variety of data types like images, vector fields and graphs. This is the development package containing the header files, and pkg-config script, and man pages.

VolPack is a software library for fast, high-quality volume rendering with this features:

• Renders data sampled on a regular, three-dimensional grid.
• Supports user-specified transfer functions for both opacity and color.
• Provides a shading model with directional light sources, multiple material types with different reflective properties, depth cueing, and shadows.
• Produces color (24 bits/pixel) or grayscale (8 bits/pixel) renderings, with or without an alpha channel.
• Supports arbitrary affine view transformations.
• Supports a flexible data format that allows an arbitrary C structure to be associated with each voxel.

This is the development package.

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.

Development headers

Das Visualization Toolkit (VTK) ist ein quelloffenes Softwaresystem für 3D-Computergrafik, Bildverarbeitung und Visualisierung.

Dieses Paket stellt die VTK-Header-Dateien bereit, die zum Kompilieren von C++-Programmen benötigt werden, die VTK für die 3D-Visualisierung nutzen.

Libxdf is a cross-platform C++ library for loading multimodal, multi- rate signals stored in XDF files. Libxdf is used in the biosignal viewing application SigViewer. It can also be integrated into other C++ applications.

This package contains the header files and the static library

The Berkeley Advanced Reconstruction Toolbox (BART) is a free and open-source image-reconstruction framework for Computational Magnetic Resonance Imaging.

This package provides Octave bindings for BART.

Digital communications in medicine (DICOM) is an information standard, originally created for image transfer, which now deals with a large range of medical data.

This package provides functions to read and (eventually) write DICOM files in Octave, a scientific computation software. The functions in the package are intended to have similar usage as the dicom functions in the Matlab Image Processing Toolbox. In Octave they are separate: most image package users will not use dicom, and its dependency might be considered troublesome.

This Octave add-on package is part of the Octave-Forge project.

GDF (General Dataformat for Biosignals) is intended to provide a generic storage for biosignals, such as EEG, ECG, MEG etc.

This package provides Octave bindings for libgdf.

ODIN ist ein Rahmenwerk für Magnetresonanztomographie (MRT). Es beinhaltet die komplette MRT-Werkzeugkette, von grundlegender Datenerfassung bis zur Bildrekonstruktion. Im Besonderen zielt es auf das schnelle Erzeugen der Prototypen von MRT-Sequenzen ab. Die Sequenzen können mit einer hochentwickelten objektorientierten C++-Programmierschnittstelle programmiert werden. Es enthält fortgeschrittene Werkzeuge zur Sequenzanalyse, wie das interaktive Plotten von k-dimensionalen Trajektorien, eine Benutzerschnittstelle für ein schnelles Kompilieren-Linken-Testen und einen mächtigen MRT-Simulator, der verschiedene virtuelle Muster unterstützt. Für die schnelle und flexible Bildrekonstruktion beinhaltet ODIN ein sehr weitgehend anpassbares, multithreadfähiges Rahmenwerk zur Datenverarbeitung.

This package provides Python3 bindings for BioSig library. Primary goal -- I/O interface to variety of biomedical file formats, including but not limited to SCP-ECG(EN1064), HL7aECG (FDA-XML), GDF, EDF.

BioXTAS RAW is a GUI based, Python program for reduction and analysis of small-angle X-ray solution scattering (SAXS) data. The package is designed for biological SAXS data.

BioXTAS RAW provides an alternative to closed source programs such as Primus and Scatter for primary data analysis. Because it can calibrate, mask, and integrate images it also provides an alternative to synchrotron beamline pipelines that scientists can install on their own computers and use both at home and at the beamline.

Brian ist ein zeitgesteuerter Simulator für »spiking neural networks«. Er wurde mit Schwerpunkt auf Flexibilität und Erweiterbarkeit ausgelegt, für die schnelle Entwicklung und Verfeinerung von neuronalen Modellen. Neuronale Modelle werden durch Sätze von durch den Benutzer vorgegebenen Differentialgleichungen, Schwellwert- und Rücksetzbedingungen (als Strings ausgedrückt) formuliert. Der Schwerpunkt liegt dabei vor allem in Netzwerken von »single compartment neuron«-Modellen (z.B. leaky integrate-and-fire oder Neuronen vom Hodgkin-Huxley-Typ). Die Eigenschaften umfassen:

• ein System zur Angabe von Mengen mit physikalischen Dimensionen
• exakte numerische Integration für lineare Differentialgleichungen
• Euler-, Runge-Kutta- und exponentielle Euler-Integration für nichtlineare Differentialgleichungen
• synaptische Verbindungen mit Verzögerungen
• kurzfristige und langfristige Plastizität (vom spike-timing abhängige Plastizität)
• eine Bibliothek von Standard-Modellkomponenten, einschließlich »integrate-and-fire«-Gleichungen, Synapsen und Ionenströmen
• einen Werkzeugsatz für die automatische Anpassung von »spiking neuron«-Modellen an elektrophysiologische Messdaten

DICOM to NIfTI conversion with the added ability to extract and summarize meta data from the source DICOMs. The meta data can be injected into a NIfTI header extension or written out as a JSON formatted text file.

This package provides the Python3 package.

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.

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.

Python bindings to the GDCM DICOM library.

Imageio is a Python library that provides an easy interface to read and write a wide range of image data, including animated images, video, volumetric data, and scientific formats.

This package provides the library for Python 3.

MIA comprises a set of tools, libraries, and plug-ins for general purpose 2D and 3D gray scale image processing and basic handling of triangular meshes. The libraries provide a basic infrastructure and generic algorithms, that can be specialized by specifying the appropriate plug-ins. This package provides the Python-3 bindings.

This package is designed for sensor- and source-space analysis of MEG and EEG data, including frequency-domain and time-frequency analyses and non-parametric statistics.

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.

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 the Python 3 module needed to run OpenSlide applications.

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.

pyxnat is a simple Python library that relies on the REST API provided by the XNAT platform since its 1.4 version. XNAT is an extensible database for neuroimaging data. The main objective is to ease communications with an XNAT server to plug-in external tools or Python scripts to process the data. It features:

• resources browsing capabilities
• read and write access to resources
• complex searches
• disk-caching of requested files and resources

The torchvision package consists of popular datasets, model architectures, and common image transformations for computer vision.

Vision with Generic Algorithms (VIGRA) is a computer vision library that puts its main emphasis on flexible algorithms, because algorithms represent the principle know-how of this field. The library was consequently built using generic programming as introduced by Stepanov and Musser and exemplified in the C++ Standard Template Library. By writing a few adapters (image iterators and accessors) you can use VIGRA's algorithms on top of your data structures, within your environment.

This package exports the functionality of the VIGRA library to Python3.

CAMP is a multi-purpose reflection library developed by Technogerma Systems France (http://www.tegesoft.com). It provides an abstraction for most of the high-level concepts of C++

• Classes
• Enumerations
• Properties
• Functions
• Objects
• Variables By wrapping all these concepts into abstract structures, CAMP provides an extra layer of flexibility to programs, and allow them to fully expose their data structures at runtime. Many applications can take advantage of CAMP, in order to automate tasks which would otherwise require a huge amount of work. For example, CAMP can be used to expose and edit objects' attributes into a graphical user interface. It can also be used to do automatic binding of C++ classes to script languages such as Python or Lua. Another possible application would be the serialization of objects to XML, text or binary formats. Or you can even combine all these examples to provide a powerful and consistent interface for manipulating your objects outside C++ code.

This package contains the files needed for development.

eegdev is a library that provides a unified interface for accessing various EEG (and other biosignals) acquisition systems. This interface has been designed to be both flexible and efficient. The device specific part is implemented by the means of plugins which makes adding new device backend fairly easy even if the library does not support them yet officially.

The core library not only provides to users a unified and consistent interface to the acquisition device but it also provides many functionalities to the device backends (plugins) ranging from configuration to data casting and scaling making writing new device backend an easy task.

This library is particularly useful to handle the acquisition part of a Brain Computer Interface (BCI) or any realtime multi-electrode acquisition in neurophysiological research.

This package contains the files needed to compile and link programs which use eegdev. It provides also the headers needed to develop new device plugins. The manpages and examples are shipped in this package.

FreeImage is an Open Source C/C++ library project for developers who would like to support popular graphics image formats like PNG, BMP, JPEG, TIFF and others as needed by today's multimedia applications. FreeImage is easy to use, fast, multithreading safe, and cross-platform (works both with Linux, 32 bit Windows and Mac OS X).

This package contains the headers and static libraries needed to develop programs using FreeImage.

This is the reference library for ICS (Image Cytometry Standard), an open standard for writing images of any dimensionality and data type to file, together with associated information regarding the recording equipment or recorded subject.

This package contains the libraries needed to build ICS applications.

Liblimereg automatically aligns two images with similar content to each other. Given two 2D images the algorithm returns the rigid transformation parameters detected for the best possible alignment (shift, rotation). There are also functions for a rigid image transformation (shift, rotation) and for creating a difference image out of two images.

This package contains the static library and the header file.

Niftilib ist eine Sammlung von Ein- und Ausgabebibliotheken zum Lesen und Schreiben von Dateien im NIfTi-1-Datenformat. NIfTI-1 ist ein binäres Dateiformat zum Speichern von medizinischen Bilddaten wie Magnetresonanzbildern (MRI) und funktionalen Magnetresonanztomographiebildern (fMRI) des Gehirns.

Dieses Paket enthält die Referenzdokumentation der Programmierschnittstelle der NIfTI-Bibliothek.

xdffileio is a library that provides a unified interface for writing and reading various biosignal file formats in realtime (i.e. streaming). It has been designed to provide a flexible, consistent and generic interface to all supported file formats while minimizing the overhead the function calls: the heaviest operations (type casting, scaling and formatting) are offloaded into a separated thread. This design makes its particularly suitable to be directly used in a data acquisition loop (like in electrophysiology recording or in Brain-Computer Interfaces (BCI)).

The genericity of the interface makes trivial various operations like transformation of a recorded file or its conversion to another file format. xdffileio currently supports EDF, BDF, GDF1 and GDF2 file formats and more will be added in future.

This package contains the files needed to compile and link programs which use xdffileio.

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.

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.

This package contains header files and shared library links.

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.

This package provides the Python interface for vmtk.

Emotive is an interface to a budget Emotiv EPOC EEG headset.

Bio-Formats is a standalone Java library for reading and writing life sciences image file formats. It is capable of parsing both pixels and metadata for a large number of formats, as well as writing to several formats.

Bio-Formats's primary purpose is to convert proprietary microscopy data into an open standard called the OME data model, particularly into the OME-TIFF file format.

The goals of CTK are as follows:

• Provide a unified set of basic programming constructs that are useful for medical imaging applications development
• Facilitate the exchange and combination of code and data
• Document, integrate, and adapt successful solutions
• Avoid the duplication of code and data
• Continuously extend to new tasks within the scope of the toolkit (medical imaging) without burdening existing tasks

This package provides the CTK header files required to compile C++ programs that use CTK.

OpenMEEG consists of state-of-the art solvers for forward problems in the field of MEG and EEG. Solvers are based on the symmetric Boundary Element method [Kybic et al, 2005], providing excellent accuracy, particularly for superficial cortical sources. OpenMEEG can compute four types of lead fields (EEG, MEG, Internal Potential and Electrical Impedence Tomography).

This package provides static libraries and header files.

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:

• Trestle (.tif)
• Hamamatsu (.vms, .vmu)
• Aperio (.svs, .tif)
• MIRAX (.mrxs)
• Generic tiled TIFF (.tif)

This package contains the java module needed to run OpenSlide applications.

VIA is a volumetric image analysis suite. The included libraries provide about 70 image analysis functions.

This package provides the header files and static libraries of vialib, vxlib and viaio.

Collection of various Perl module used by other MNI software packages.