Debian Science Project
Image analysis
Debian Science image analysis packages

This metapackage will install Debian Science packages related to scientific image acquisition. This might be used in several sciences (as for instance science-dataacquisition, science-viewing and science-typesetting).


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 Science 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 Science mailing list

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Debian Science Image analysis packages

Official Debian packages with high relevance

Programa de interfaz grafica para la Velocimetría de Partículas basada en Imágenes
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Gpiv es una programa de interfaz gráfica que utiliza bibliotecas GTK/ GNOME para la Velocimetría de Partículas basada en Imágenes (en inglés, PIV). El programa proporciona una visión general para la configuración de parámetros en los procesos, y permite cambiarlos fácilmente, ejecutar los procesos, individualmente o en cadena, visualizar y mostrar los resultados. Gpiv puede invocar los siguientes procesos:

Procesamiento de imágenes: manipulaciones típicas de imágenes que podrían ser usadas para interrogaciones PIV.

Interrogación de imágenes, da como resultado unas estimaciones de los desplazamientos de las imágenes de las partículas.

Validación de datos para probar en valores no comunes, efecto de bloqueo en el valor máximo y gradientes de velocidad en las áreas de interrogación.

Post procesamiento de datos: manipulación de datos, escalado temporal y espacial para obtener un campo de velocidades a partir de los datos PIV, cálculo de promedios espaciales, vorticidad y contracción.

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command line programs for Particle Image Velocimetry
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A collection of programs for images that are generated during a Particle Image Velocimetry (PIV) experiment. This is a technique to obtain the velocity field of a fluid flow quantitatively and is performed by tracking tracer particles that have been seeded to a fluid. The technique is also applied for observing deformations at surfaces of (solid) bodies. The package contains:

  • an image processing program for typical filtering and manipulation routines that may be convenient for PIV.
  • an image interrogation program resulting into estimators of particle image displacements.
  • validation programs to test on outliers, peak-locking effect and velocity gradients.
  • post-processing programs for data manipulation (flipping, rotation etc), spatial and time scaling, calculation of spatial averages and derivative quantities from the PIV data, like vorticity and strain.
  • miscellaneous programs and scripts to perform image format conversion, batch-processing, pipeline processing (image evaluation, validation and post-processing at once), calculation of time averages from a series of PIV data sets, data-visualization and data-manipulation.

All programs start with gpiv_.

This package contains all files used by gpivtools and gpivtools-mpi, like the man pages.

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.

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: SciCrunch  OMICtools 
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Lightweight Image Registration
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Command line application for image registration. Automatically finds an optimal alignment of two input images, that makes both most similar to each other. Outputs the rigid transformation parameters (shift and rotation) and/or the registered (transformed/aligned) image.

Fast algorithm based on analytical derivative based optimization with a multilevel approach and without expensive sparse-matrices.

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Tools to process and visualize scientific data and images - command line tools
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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.

*Popularitycontest results: number of people who use this package regularly (number of people who upgraded this package recently) out of 200836