Debian Med Project
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Summary
Imaging
Debian Med image processing and visualization packages

This metapackage will install Debian packages which might be useful in medical image processing and visualization.

On one hand, it installs several packages supporting various image file formats and image management, like DICOM (Digital Imaging and Communications in Medicine) which is the de-facto standard for medical image management, and NIFTI. On the other hand, it provides a variety of software packages that can be used for visualization and for image processing - either from a graphical user interface, the command line, or implemented in workflows.

Description

For a better overview of the project's availability as a Debian package, each head row has a color code according to this scheme:

If you discover a project which looks like a good candidate for Debian Med to you, or if you have prepared an unofficial Debian package, please do not hesitate to send a description of that project to the Debian Med mailing list

Links to other tasks

Debian Med Imaging packages

Official Debian packages with high relevance

Aeskulap
medical image viewer and DICOM network client
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Aeskulap is able to load a series of special images stored in the DICOM format for review. Additionally it is able to query and fetch DICOM images from archive nodes (also called PACS) over the network. Aeskulap tries to achieve a full open source replacement for commercially available DICOM viewers.

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Amide
software for Medical Imaging
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AMIDE: (Amide's a Medical Imaging Data Examiner) AMIDE is a tool for viewing and analyzing medical image data sets. It's capabilities include the simultaneous handling of multiple data sets imported from a variety of file formats, image fusion, 3D region of interest drawing and analysis, volume rendering, and rigid body alignments.

Amide imports most clinical DICOM files (using the DCMTK library).

Please cite: Andreas Markus Loening and Sanjiv Sam Gambhir: AMIDE: A Free Software Tool for Multimodality Medical Image Analysis. (PubMed) Molecular Imaging 2(3):131-7 (2003)
Screenshots of package amide
Caret
Computerized Anatomical Reconstruction and Editing Toolkit
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This software allows for creating, viewing and manipulating surface reconstructions of the cerebral and cerebellar cortex, viewing volumes and for displaying experimental data on the surfaces and volumes. While Caret is primarily a GUI application with 'caret_command' there is also a versatile command line tool, that allows access to a substantial proportion of Caret's functionality.

Caret can download and use stereotaxic atlases (human, monkey, mouse and rat) from an open online database.

Some functionality of Caret is only available when additional data files, provided by the caret-data package, are available. This includes:

  • Map volumes to surface via PALS atlas
  • Multi-resolution morphing
  • Projection of foci via PALS atlas
  • Surface-based registration
  • Surface flattening

Currently the caret-data package is only available from the NeuroDebian repository. Please see http://neuro.debian.net for more information.

Please cite: David C. Van Essen, Heather A. Drury, James Dickson, John Harwell, Donna Hanlon and Charles H. Anderson: An Integrated Software Suite for Surface-based Analyses of Cerebral Cortex. (PubMed,eprint) Journal of American Medical Informatics Association 8(5):443-459 (2001)
Ctn
Central Test Node, a DICOM implementation for medical imaging
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DICOM is the standard for image storage, annotation, and networking. It is used widely for medical imaging. The Central Test Node software (CTN) provides an implementation of this standard.

This package includes the binary and run-time configuration files for CTN.

Please cite: S.M. Moore, S.A. Hoffman and D.E. Beecher: DICOM Shareware: A Public Implementation of the DICOM Standard 2165:772–781 (1994)
Ctsim
Computed tomography simulator
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CTSim provides an interactive computed tomography simulator. Computed tomography is the technique of estimating the interior of an object by measuring x-ray absorption through that object.

CTSim has both command-line tools and a graphical user interface. CTSim has very educational trace modes for viewing the data collection simulation as well as the reconstruction.

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Dcmtk
OFFIS DICOM toolkit command line utilities
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DCMTK includes a collection of libraries and applications for examining, constructing and converting DICOM image files, handling offline media, sending and receiving images over a network connection, as well as demonstrative image storage and worklist servers.

This package contains the DCMTK utility applications.

Note: This version was compiled with libssl support.

Dicom3tools
DICOM medical image files manipulation and conversion tools
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Command line utilities for creating, modifying, dumping and validating files of DICOM attributes. Support conversion of some proprietary medical image formats to DICOM. Can handle older ACR/NEMA format data, and some proprietary versions of that such as SPI.

Dicomnifti
converts DICOM files into the NIfTI format
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The dinifti program converts MRI images stored in DICOM format to NIfTI format. The NIfTI format is thought to be the new standard image format for medical imaging and can be used with for example with FSL, AFNI, SPM, Caret or Freesurfer.

dinifti converts single files, but also supports fully automatic batch conversions of complete dicomdirs. Additionally, converted NIfTI files can be properly named, using image series information from the DICOM files.

Dicomscope
OFFIS DICOM Viewer
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DICOMscope is a free DICOM viewer which can display uncompressed, monochrome DICOM images from all modalities and which supports monitor calibration according to DICOM part 14 as well as presentation states.

DICOMscope offers a print client (DICOM Basic Grayscale Print Management) which also implements the optional Presentation LUT SOP Class.

The development of this prototype was commissioned by the "Committee for the Advancement of DICOM" and demonstrated at the European Congress of Radiology ECR 1999. An enhanced version was developed for the "DICOM Display Consistency Demonstration" at RSNA InfoRAD 1999.

The current release has been demonstrated at ECR 2001 and contains numerous extensions, including a print server, support for encrypted DICOM communication, digital signatures and structured reporting.

Fslview
viewer for (f)MRI and DTI data
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This package provides a viewer for 3d and 4d MRI data as well as DTI images. FSLView is able to display ANALYZE and NIFTI files. The viewer supports multiple 2d viewing modes (orthogonal, lightbox or single slices), but also 3d volume rendering. Additionally FSLView is able to visualize timeseries and can overlay metrical and stereotaxic atlas data.

FSLView is part of FSL.

Please cite: S.M. Smith, M. Jenkinson, M.W. Woolrich, C.F. Beckmann, T.E.J. Behrens, H. Johansen-Berg, P.R. Bannister, M. De Luca, I. Drobnjak, D.E. Flitney, R. Niazy, J. Saunders, J. Vickers, Y. Zhang, N. De Stefano, J.M. Brady and P.M. Matthews: Advances in functional and structural MR image analysis and implementation as FSL. (PubMed) NeuroImage 23:208-219 (2004)
Remark of Debian Med team: fslview was removed from Debian (see #647810)

The bug log (http://bugs.debian.org/647810) explains the reasons for the removal. The maintainers did never respond whether they plan to bring back a more recent version of this package

Ginkgocadx
Medical Imaging Software and complete DICOM Viewer
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Ginkgo CADx provides a complete DICOM viewer solution with advanced capabilities and support for extensions.

  • Easy and customizable interface through profiles.
  • Full featured DICOM image visualization.
  • Complete tool set (measure, markers, text, ...).
  • Multiple modalities support (Neurological, Radiological, Dermatological, Ophthalmological, Ultrasound, Endoscopy, ...)
  • Dicomization support from JPEG, PNG, GIF and TIFF.
  • Full EMH integration support: HL7 standard and IHE compliant workflows.
  • PACS Workstation (C-FIND, C-MOVE, C-STORE...)
  • Extensible through custom extensions.
  • Retinal image mosaic composition.
  • Automatic retinal analysis diagnostics.
  • Psoriasis automatic diagnostics.
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Gwyddion
Scanning Probe Microscopy visualization and analysis tool
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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.

Gwyddion's Python scripting interface Pygwy is also included.

Please cite: David Nečas and Petr Klapetek: Gwyddion: an open-source software for SPM data analysis. (eprint) Central European Journal of Physics 10(1):181-188 (2012)
Registry entries: RRID  OMICtools 
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Imagej
Image processing program with a focus on microscopy images
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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.

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Imagevis3d
desktop volume rendering application for large data
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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).

Libgdcm-tools
Grassroots DICOM tools and utilities
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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, gdcmconv, gdcmdiff, gdcmdump, gdcmpap3, gdcmgendir, gdcmimg, gdcminfo, gdcmpdf, gdcmraw, gdcmscanner, gdcmscu, gdcmtar, gdcmxml programs.

Please cite: David Rodríguez González, Trevor Carpenter, Jano I. van Hemert and Joanna Wardlaw: An open source toolkit for medical imaging de-identification. (PubMed,eprint) European Radiology 20(8):1896-1904 (2010)
Lipsia
analysis suite for MRI and fMRI data
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Leipzig Image Processing and Statistical Inference Algorithms (LIPSIA)

This is a software package for the data processing and evaluation of functional magnetic resonance images. The analysis of fMRI data comprises various aspects including filtering, spatial transformation, statistical evaluation as well as segmentation and visualization. All these aspects are covered by LIPSIA. For the statistical evaluation, a number of well established and peer-reviewed algorithms were implemented in LIPSIA that allow an efficient and user-friendly processing of fMRI data sets. As the amount of data that must be handled is enormous, an important aspect in the development of LIPSIA was the efficiency of the software implementation.

LIPSIA operates exclusively on data in the VISTA data format. However, the package contains converters for medical image data in iBruker, ANALYZE and NIfTI format -- converting VISTA images into NIfTI files is also supported.

Remark of Debian Med team: lipsia was removed from Debian (see #674295)

The bug log (http://bugs.debian.org/674295) explains the reasons for the removal and the conditions when a new version might be back

Medcon
Medical Image (DICOM, ECAT, ...) conversion tool
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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.

Minc-tools
MNI medical image format tools
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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.

Nifti-bin
tools shipped with the NIfTI library
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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).

Odin
develop, simulate and run magnetic resonance sequences
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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.

Please cite: Thies H. Jochimsen, Michael von Mengershausen: ODIN: Object-oriented development interface for NMR. (2004)
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Openslide-tools
Manipulation and conversion tools for OpenSlide
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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.

Pixelmed-apps
DICOM implementation containing Image Viewer and a ECG Viewer - jnlp
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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

Python-dicom
DICOM medical file reading and writing (Python 2)
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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 2.

Python-mvpa2
multivariate pattern analysis with Python v. 2
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PyMVPA eases pattern classification analyses of large datasets, with an accent on neuroimaging. It provides high-level abstraction of typical processing steps (e.g. data preparation, classification, feature selection, generalization testing), a number of implementations of some popular algorithms (e.g. kNN, Ridge Regressions, Sparse Multinomial Logistic Regression), and bindings to external machine learning libraries (libsvm, shogun).

While it is not limited to neuroimaging data (e.g. fMRI, or EEG) it is eminently suited for such datasets.

This is a package of PyMVPA v.2. Previously released stable version is provided by the python-mvpa package.

The package is enhanced by the following packages: python-mdp python-sklearn
Python-nibabel
Python bindings to various neuroimaging data formats
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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.

This package also provides a commandline tools:

  • dicomfs - FUSE filesystem on top of a directory with DICOMs
  • nib-ls - 'ls' for neuroimaging files
  • parrec2nii - for conversion of PAR/REC to NIfTI images
Python-nipy
Analysis of structural and functional neuroimaging data
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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
Python-nipype
Neuroimaging data analysis pipelines in Python
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Nipype interfaces Python to other neuroimaging packages and creates an API for specifying a full analysis pipeline in Python. Currently, it has interfaces for SPM, FSL, AFNI, Freesurfer, but could be extended for other packages (such as lipsia).

Please cite: SS Ghosh, C Burns, D Clark, K Gorgolewski, YO Halchenko, C Madison, R Tungaraza and KJ Millman: Nipype: Opensource platform for unified and replicable interaction with existing neuroimaging tools (eprint) 16th Annual Meeting of the Organization for Human Brain Mapping :106 (2010)
Python-nitime
timeseries analysis for neuroscience data (nitime)
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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.

Slicer
software package for visualization and image analysis - main application
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Slicer is an application for computer scientists and clinical researchers. The platform provides functionality for segmentation, registration and three-dimensional visualization of multi-modal image data, as well as advanced image analysis algorithms for diffusion tensor imaging, functional magnetic resonance imaging and image-guided therapy. Standard image file formats are supported, and the application integrates interface capabilities to biomedical research software and image informatics frameworks.

3D Slicer main application.

Remark of Debian Med team: slicer was removed from Debian (see #644352)

The bug log (http://bugs.debian.org/644352) explains the reasons for the removal and the conditions when a new version might be back

Sofa-apps
GUI for the Simulation Open Framework Architecture (SOFA)
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SOFA is an Open Source framework primarily targeted at real-time simulation, with an emphasis on medical simulation. It is mostly intended for the research community to help develop newer algorithms, but can also be used as an efficient prototyping tool.

This package contains the SOFA main application.

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Via-bin
tools for volumetric image analysis
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VIA is a volumetric image analysis suite for functional and structural (medical) images. The suite consists of different tools ranging from simple data handling over viewers to complex image transformation.

All tools operate on data in VISTA format. The package contains several converters from e.g. PNG, PGM or PNM to this data format and back.

Xmedcon
Medical Image (DICOM, ECAT, ...) conversion tool (GUI)
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This project stands for Medical Image Conversion. Released under the (L)GPL, it comes with the full C-source code of the library, a flexible command line utility and a neat graphical front-end using the GTK+ toolkit. The currently supported formats are: Acr/Nema 2.0, Analyze (SPM), DICOM 3.0, InterFile 3.3 and PNG.

The program also allows one to read unsupported files without compression, to print pixel values or to extract/reorder specified images. It is possible to retrieve the raw binary/ascii image arrays or to write PNG for desktop applications.

This is the program version for X based on GTK+. Processes only one file at a time.

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Official Debian packages with lower relevance

Imagemagick
image manipulation programs -- binaries
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ImageMagick is a software suite to create, edit, and compose bitmap images. It can read, convert and write images in a variety of formats (over 100) including DPX, EXR, GIF, JPEG, JPEG-2000, PDF, PhotoCD, PNG, Postscript, SVG, and TIFF. Use ImageMagick to translate, flip, mirror, rotate, scale, shear and transform images, adjust image colors, apply various special effects, or draw text, lines, polygons, ellipses and Bézier curves. All manipulations can be achieved through shell commands as well as through an X11 graphical interface (display).

This package include links to channel depth specific binaries and manual pages.

This is a dummy package. You can safely purge or remove it.

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Imview
Image viewing and analysis application
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Imview is an application which

  • Displays a large number of image formats.
  • Displays 2D or 3D (as slices) images with a very good zoom and pan feature.
  • Works with multi-spectral, time series or multi-page documents (e.g.: Satellite images, TIFF stacks, animated GIFs and heterogeneous multi-component files).
  • Displays all pixel types (1-bit to 64-bit data, integer or floating point).
  • Arbitrary 1-D profile of 2-D images (or of 2-D slices of 3-D images) can be displayed.
  • Has support for arbitrary colourmaps for all pixel types (i.e.: false colour display).
  • Has standard image manipulation facilities (brightness/contrast, gamma, zoom, crop, rotation, etc).
  • Can be controlled remotely via sockets and text commands (for easy integration into various image analysis systems).
  • Images can be uploaded into Imview via sockets or shared memory.
  • And much more!
Please cite: Hugues Talbot: ImView: a portable image display application (eprint)
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Pngquant
PNG (Portable Network Graphics) image optimising utility
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Debtags of package pngquant:
interfacecommandline
roleprogram
scopeutility
usecompressing, converting
works-withimage, image:raster
works-with-formatpng
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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.

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Trimage
GUI and command-line interface to optimize image files
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interfacecommandline, x11
roleprogram
scopeutility
uitoolkitqt
works-withimage
works-with-formatjpg, png
x11application
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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.

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Debian packages in contrib or non-free

Fsl
transitional dummy package
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interfacecommandline, x11
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The only purpose of this package is to enable upgrades to the new 'fsl-core' package which replaces 'fsl'. This package can safely be removed.

Users aiming to perform a complete FSL installation (including all data components) are advised to install the 'fsl-complete' package from NeuroDebian.

Please cite: Mark Jenkinson, Christian F. Beckmann, Timothy E. J. Behrens, Mark W. Woolrich and Stephen M. Smith: FSL. (PubMed) NeuroImage 62(2):782-790 (2012)
Vmtk
the Vascular Modeling Toolkit
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Newer upstream!
License: non-free
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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.

*Popularitycontest results: number of people who use this package regularly (number of people who upgraded this package recently) out of 203532