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bioformats

Bio-Formats is a Java library for reading and writing data in life sciences image file formats. It is developed by the Open Microscopy Environment (particularly UW-Madison LOCI and Glencoe Software). Bio-Formats is released under the GNU General Public License (GPL); commercial licenses are available from Glencoe Software.

ckanext-dcat

CKAN ♥ DCAT

d3

A JavaScript visualization library for HTML and SVG.

design

epos-dcat-ap

DCAT-AP extension for EPOS Solid Earth Data

epos_dcat-ap

etlhelper

ETL Helper is a Python library to simplify data transfer between databases.

imagej-omero

Server- and client-side communication between ImageJ and OMERO

mapper

OpenOrienteering Mapper is a software for creating maps for the orienteering sport.

mathics

a general-purpose computer algebra system

mtools

Image analysis tools in Matlab working with data in an OMERO server

nanoclust

NanoCLUST is an analysis pipeline for UMAP-based classification of amplicon-based full-length 16S rRNA nanopore reads

nanopype

Snakemake pipelines for nanopore sequencing data archiving and processing

ome-documentation

Sphinx-based documentation for the Open Microscopy Environment

omero-install

OMERO installation scripts

omero-setup

Simple data-import bootstrap for daily testing.

openmicroscopy

OME (Open Microscopy Environment) develops open-source software and data format standards for the storage and manipulation of biological light microscopy data. A joint project between universities, research establishments and industry in Europe and the USA, OME has over 20 active researchers with strong links to the microscopy community. Funded by private and public research grants, OME has been a major force on the international microscopy stage since 2000.

ou-tm351

WIP site - issue tracker

presentations

HTML-based presentations from the OME team.

pygeoapi

pygeoapi is a Python server implementation of the OGC API suite of standards. The project emerged as part of the next generation OGC API efforts in 2018 and provides the capability for organizations to deploy a RESTful OGC API endpoint using OpenAPI, GeoJSON, and HTML. pygeoapi is open source and released under an MIT license.

pytest-rerunfailures

a py.test plugin that re-runs failed tests up to -n times to eliminate flakey failures

qxw

c crossword puzzle creator

rbioformats

R interface to the Bio-Formats library

scripts

Extracted OmeroPy/scripts directory for local modifications.

shacl

SHACL API in Java based on Apache Jena

shapely

Manipulation and analysis of geometric objects

shell-tools

Useful shell scripts and other tools for sysadmin, docker, etc

snoopycrimecop

OME tools for managing the git(hub) workflow

snoopys-sandbox

Test repository for the snoopycrimecop/snoopycrimecop code.

snoopys-sandbox-2

Submodule for snoopy-sandbox for properly testing scc.py