Debian Med Project
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Debian Med suggestions for medical laboratories

This metapackage contains dependencies for software and that could be useful ro run a medical laboratory.


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

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Debian Med Laboratory packages

Official Debian packages with high relevance

count cell colonies (CFUs) on agar plates by processing digital pictures
Versions of package opencfu
Popcon: 1 users (1 upd.)*
Versions and Archs
License: DFSG free

OpenCFU is a completely open source lightweight application designed to enumerate clustered circular objects such as bacterial colonies. It can handle digital pictures as well as live stream from a video device/webcam. OpenCFU is cross-platform, fast, reliable and allows the user to implement intuitive filters.

Whole-slide imaging support for Orthanc (digital pathology)
Versions of package orthanc-wsi
Popcon: 72 users (10 upd.)*
Versions and Archs
License: DFSG free

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.

Please cite: Sebastien Jodogne: The Orthanc Ecosystem for Medical Imaging. J Digit Imaging (2018)

Packaging has started and developers might try the packaging code in VCS

Laboratory analysis, research and investigation software application
Versions of package openfreezer
Versions and Archs
License: GPL-3+
Debian package not available
Version: 20131306-1

OpenFreezer Laboratory Reagent Tracking and Workflow Management System is an open-source information management system for biological laboratories. The system tracks information on all reagents within the laboratory, including specific properties of each reagent (i.e. sequences, external identifiers), and on all the physical preparations of these reagents (storage locations, physical characteristics). Complementing this repository are workflow tools, such as primer design and automated feature mapping, making OpenFreezer a valuable tool for the bench scientist.

Please cite: Marina Olhovsky, Kelly Williton, Anna Yue Dai, Adrian Pasculescu, John Paul Lee, Marilyn Goudreault, Clark D. Wells, Jin Gyoon Park, Anne-Claude Gingras, Rune Linding, Tony Pawson and Karen Colwill": OpenFreezer: a reagent information management software system. (PubMed) Nature Methods 8(8):612–613 (2011)

No known packages available

tool for biospecimen inventory management
License: to be clarified
Debian package not available

CaTissue Suite is caBIG's biorepository tool for biospecimen inventory management, tracking, and annotation. This tool permits users to enter and retrieve data concerning the collection, storage, quality assurance, and distribution of biospecimens. caTissue Suite is sufficiently scalable and configurable for deployment across biospecimen resources of varying size and function, and that manage multiple types of biospecimens (tissue, biofluids, nucleic acid). The tool provides search functionality for both the biorepository staff and research scientist, who may be interested in searching for and requesting biospecimens for correlative science studies.

caTissue Suite features include:

  • Customizable user roles and privileges structure to support multiple, independent repositories within a single caTissue installation.
  • Collection Protocol template creation allows representation of pre-defined specimen processing schemes and multiple study arms and time points in order to expedite data entry.
  • Patient study registration with duplicate patient checking algorithm.
  • Facilitated specimen accessioning, recording of processing events, creation and recording of biospecimen derivatives and aliquots.
  • Recording of biospecimen shipping and tracking events across repositories in a single caTissue installation.
  • Improved data form display for custom annotations (Dynamic Extensions tool), including new CAP checklist based forms for pathology annotation of major organ systems.
  • caTIES-like pathology report text annotation.
  • Advanced Query “Wizard”, allowing for the creation and saving of complex queries which can be run as pre-defined or parameterized searches.
  • Searches based on temporal relationships.
  • Specimen requisition and request tracking.
Enterprise Laboratory Information System
License: UIRF Open-source Based Public Software License
Debian package not available

OpenELIS is a robust Enterprise Laboratory Information System built around an extensible and scalable framework. OpenELIS is designed and developed through the collaborative efforts of Public Health Laboratories to accommodate business processes that are common to all public health laboratories; encompassing clinical, environmental, newborn screening, and animal testing.

The goal of the OpenELIS team is to develop a state of the art system that is economically sustainable by reducing both initial investment and ongoing maintenance costs. By using an open source approach, we ensure that the project will continue to evolve and meet the changing needs of the community.

*Popularitycontest results: number of people who use this package regularly (number of people who upgraded this package recently) out of 235225