Summary
Laboratory
Debian Med suggestions for medical laboratories
This metapackage contains dependencies for software and that could
be useful ro run a medical laboratory.
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
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Debian Med Laboratory packages
Official Debian packages with high relevance
opencfu
count cell colonies (CFUs) on agar plates by processing digital pictures
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Versions of package opencfu |
Release | Version | Architectures |
sid | 4.0.0+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 3.9.0-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 3.9.0-3 | amd64,arm64,armhf,i386 |
bullseye | 4.0.0-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 4.0.0+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 4.0.0+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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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.
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orthanc-wsi
Whole-slide imaging support for Orthanc (digital pathology)
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Versions of package orthanc-wsi |
Release | Version | Architectures |
bullseye | 1.0-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.1-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 2.0+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 2.0+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 0.6-2 | amd64,arm64,armhf,i386 |
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License: DFSG free
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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.
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Packaging has started and developers might try the packaging code in VCS
openfreezer
Laboratory analysis, research and investigation software application
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Versions of package openfreezer |
Release | Version | Architectures |
VCS | 20131306-1 | all |
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License: GPL-3+
Debian package not available
Version: 20131306-1
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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)
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No known packages available
catissuesuite
tool for biospecimen inventory management
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License: to be clarified
Debian package not available
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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.
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openelis
Enterprise Laboratory Information System
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License: UIRF Open-source Based Public Software License
Debian package not available
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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.
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