GitHub topics: omero

Repositories

Cellular-Imaging-Amsterdam-UMC/NL-BIOMERO Fork of ome/docker-example-omero-grid

Multi-container OMERO with BIOMERO for AMC

Language: Python - Size: 240 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 5 - Forks: 2

ome/omero-py

Python project containing Ice remoting code for OMERO

Language: Python - Size: 11.3 MB - Last synced at: 1 day ago - Pushed at: 10 days ago - Stars: 23 - Forks: 35

ome/omero-figure

An OMERO.web app for creating Figures from images in OMERO

Language: JavaScript - Size: 8.35 MB - Last synced at: 7 days ago - Pushed at: 10 days ago - Stars: 17 - Forks: 32

TheJacksonLaboratory/ezomero

A module with convenience functions for writing Python code that interacts with OMERO.

Language: Python - Size: 1.28 MB - Last synced at: 8 days ago - Pushed at: 11 days ago - Stars: 44 - Forks: 15

ome/omero-documentation

Sphinx-based documentation for the Open Microscopy Environment

Language: Python - Size: 233 MB - Last synced at: 1 day ago - Pushed at: 11 days ago - Stars: 22 - Forks: 51

ome/omero-python-superbuild

OMERO build for Python server components

Size: 433 KB - Last synced at: 8 days ago - Pushed at: 12 days ago - Stars: 0 - Forks: 4

ome/omero-cli-zarr

Language: Python - Size: 350 KB - Last synced at: 8 days ago - Pushed at: 13 days ago - Stars: 16 - Forks: 10

ome/devspace

Continuous integration tool for OME projects

Language: Shell - Size: 859 KB - Last synced at: 8 days ago - Pushed at: 17 days ago - Stars: 18 - Forks: 18

BIOP/ArgoLight_analysis_tool

Code to control the quality of images taken with our microscopes

Language: Java - Size: 17.3 MB - Last synced at: 17 days ago - Pushed at: 17 days ago - Stars: 2 - Forks: 1

ome/docker-example-omero

OMERO Docker compose example

Language: Shell - Size: 21.5 KB - Last synced at: 8 days ago - Pushed at: about 1 year ago - Stars: 26 - Forks: 29

ome/omero-server-docker

OMERO.server production docker image

Language: Shell - Size: 163 KB - Last synced at: 8 days ago - Pushed at: 18 days ago - Stars: 14 - Forks: 28

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.

Language: Java - Size: 1.85 GB - Last synced at: 1 day ago - Pushed at: 18 days ago - Stars: 210 - Forks: 102

ome/omero-build

OMERO top-level build for all components

Language: Dockerfile - Size: 995 KB - Last synced at: 8 days ago - Pushed at: 18 days ago - Stars: 1 - Forks: 7

ome/omero-model

Gradle project for generating model jar for OMERO

Language: Java - Size: 6.66 MB - Last synced at: 1 day ago - Pushed at: 19 days ago - Stars: 0 - Forks: 13

ome/omero-metadata

OMERO plugin for metadata manipulation https://www.openmicroscopy.org/omero/

Language: Python - Size: 479 KB - Last synced at: 8 days ago - Pushed at: 19 days ago - Stars: 8 - Forks: 13

WU-BIMAC/W-IDM_OmeroImporterExcelHelperPy

This repository contains Python software that was created to explore file system directories and automatically collect the names of image data files to be annotated with experimental and sample preparation metadata and imported into OMERO.

Language: Python - Size: 603 KB - Last synced at: 20 days ago - Pushed at: 20 days ago - Stars: 2 - Forks: 1

BIOP/OMERO-scripts

Series of script to make use of OMERO

Language: Groovy - Size: 519 KB - Last synced at: 20 days ago - Pushed at: 20 days ago - Stars: 2 - Forks: 2

ome/omero-gateway-java

Gradle project containing OMERO Java Client Library

Language: Java - Size: 1.21 MB - Last synced at: 7 days ago - Pushed at: 22 days ago - Stars: 1 - Forks: 9

manics/kubernetes-omero

Kubernetes Helm charts for OMERO

Language: Python - Size: 1.76 MB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 9 - Forks: 11

NL-BioImaging/biomero

BIOMERO - A python library for easy connecting between OMERO (jobs) and a Slurm cluster

Language: Python - Size: 4.5 MB - Last synced at: 8 days ago - Pushed at: 24 days ago - Stars: 14 - Forks: 4

ome/omero-blitz

Gradle project containing Ice remoting code for OMERO

Language: Java - Size: 8.88 MB - Last synced at: 1 day ago - Pushed at: 25 days ago - Stars: 0 - Forks: 15

ome/omero-server

Gradle project containing main server logic for OMERO

Language: Java - Size: 5.72 MB - Last synced at: 1 day ago - Pushed at: 25 days ago - Stars: 6 - Forks: 14

ome/omero-downloader

An OMERO client for downloading data in bulk from the server.

Language: Java - Size: 322 KB - Last synced at: 8 days ago - Pushed at: over 1 year ago - Stars: 5 - Forks: 5

ome/omero-renderer

Gradle project containing rendering functionality for OMERO

Language: Java - Size: 861 KB - Last synced at: 8 days ago - Pushed at: 25 days ago - Stars: 0 - Forks: 10

ome/omero-romio

Gradle project for the ROMIO library of OMERO

Language: Java - Size: 586 KB - Last synced at: 8 days ago - Pushed at: 25 days ago - Stars: 0 - Forks: 13

ome/omero-common

Gradle project containing common utilities for OMERO

Language: Java - Size: 1.75 MB - Last synced at: 8 days ago - Pushed at: 25 days ago - Stars: 1 - Forks: 11

tlambert03/napari-omero

Browse your OMERO database from within napari.

Language: Python - Size: 9.66 MB - Last synced at: 14 days ago - Pushed at: 25 days ago - Stars: 36 - Forks: 14

TheJacksonLaboratory/jax-omerometrics

Repo for generating OMERO reports/dashboards

Language: Python - Size: 25.4 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 1 - Forks: 0

ome/omero-scripts

Core OMERO Scripts

Language: Python - Size: 1.83 MB - Last synced at: 8 days ago - Pushed at: about 1 month ago - Stars: 12 - Forks: 33

ome/omero-blitz-plugin

Build tool for generating remoting code in OMERO

Language: Groovy - Size: 117 KB - Last synced at: 8 days ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 4

ome/omero-gradle-plugins

Super-project of all gradle plugins for OMERO

Language: Dockerfile - Size: 87.9 KB - Last synced at: 8 days ago - Pushed at: about 1 month ago - Stars: 1 - Forks: 9

ome/omero-web

Django-based OMERO.web client

Language: Python - Size: 25.2 MB - Last synced at: 1 day ago - Pushed at: 20 days ago - Stars: 18 - Forks: 31

ome/omero-marshal

OMERO marshalling infrastructure

Language: Python - Size: 415 KB - Last synced at: 8 days ago - Pushed at: 5 months ago - Stars: 4 - Forks: 11

ome/omero-rois

OMERO python ROI utils

Language: Python - Size: 85 KB - Last synced at: 8 days ago - Pushed at: 20 days ago - Stars: 3 - Forks: 5

WEHI-SODA-Hub/OmeroCrate

Tools for uploading an RO-Crate dataset to Omero

Language: Python - Size: 873 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

ome/omero-install

OMERO installation scripts

Language: Shell - Size: 1.12 MB - Last synced at: 7 days ago - Pushed at: about 2 months ago - Stars: 4 - Forks: 24

BiologyTools/Bio

A .NET library & program for annotating, & editing various microscopy imaging formats using Bioformats supported images. including whole slide, pyramidal & series.

Language: C# - Size: 28.9 MB - Last synced at: 17 days ago - Pushed at: over 2 years ago - Stars: 6 - Forks: 0

ome/omero-certificates

OMERO server certificate management plugin

Language: Python - Size: 124 KB - Last synced at: 8 days ago - Pushed at: 20 days ago - Stars: 0 - Forks: 7

ome/omero-iviewer

An OMERO.web app allowing to view images

Language: JavaScript - Size: 12.4 MB - Last synced at: 7 days ago - Pushed at: 2 months ago - Stars: 19 - Forks: 30

NFDI4BIOIMAGE/omero-vitessce

OMERO.web plugin for the Vitessce multimodal data viewer.

Language: Python - Size: 41.3 MB - Last synced at: 5 days ago - Pushed at: 2 months ago - Stars: 5 - Forks: 0

MontpellierRessourcesImagerie/OMERO-metrics

OMERO-metrics is an omero web app to analyze and visualize microscope metrology data

Language: Python - Size: 30.1 MB - Last synced at: about 1 month ago - Pushed at: 3 months ago - Stars: 1 - Forks: 3

NFDI4BIOIMAGE/omero-kg-benchmark

Repository for subproject P4 "Endpoint Drafting and Testing", part of project "Increasing interoperability of bioimage dataset resources"at the 2024 deNBI BioHackathon

Language: Jupyter Notebook - Size: 11.3 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

ome/rOMERO-gateway

OMERO R Gateway

Language: R - Size: 375 KB - Last synced at: 8 days ago - Pushed at: over 1 year ago - Stars: 6 - Forks: 10

BiologyTools/BioLib

A GUI-less version of Bio .NET library for editing & annotating various microscopy image formats. Supports all bioformats supported images. Integrates with ImageJ, running ImageJ filters & macro functions.

Language: C# - Size: 65.2 MB - Last synced at: 17 days ago - Pushed at: 3 months ago - Stars: 3 - Forks: 1

BiologyTools/OMERO.NET

OMERO converted to .NET with IKVM.

Language: C# - Size: 141 MB - Last synced at: 17 days ago - Pushed at: 3 months ago - Stars: 3 - Forks: 0

ome/prod-playbooks

Playbooks used by the OME team for deploying production services including OMERO

Language: Jinja - Size: 1.31 MB - Last synced at: 7 days ago - Pushed at: 3 months ago - Stars: 4 - Forks: 18

ome/omero-plugins

Collection of OMERO extensions (plugins, apps)

Size: 575 KB - Last synced at: 8 days ago - Pushed at: 2 months ago - Stars: 0 - Forks: 7

ome/omero-guides

Guides for using OMERO

Language: Python - Size: 972 KB - Last synced at: 8 days ago - Pushed at: 4 months ago - Stars: 1 - Forks: 5

ome/omero-cli-transfer

An OMERO CLI plugin for creating transfer packets between OMERO servers.

Language: Python - Size: 3.48 MB - Last synced at: 8 days ago - Pushed at: 4 months ago - Stars: 17 - Forks: 15

ome/omero-prometheus-tools

Utilities for monitoring OMERO with Prometheus

Language: Python - Size: 68.4 KB - Last synced at: 8 days ago - Pushed at: 4 months ago - Stars: 2 - Forks: 9

ome/omero-signup

OMERO.web app to allow anyone to signup for an OMERO account

Language: Python - Size: 104 KB - Last synced at: 8 days ago - Pushed at: 4 months ago - Stars: 1 - Forks: 7

ome/omero-ms-zarr

Experimental micro-service for implementing the Zarr spec over HTTP

Language: Java - Size: 354 KB - Last synced at: 8 days ago - Pushed at: 20 days ago - Stars: 18 - Forks: 12

ome/omero-cli-render

OMERO command-line tool for rendering

Language: Python - Size: 425 KB - Last synced at: 8 days ago - Pushed at: 5 months ago - Stars: 2 - Forks: 10

SaibotMagd/RDM_system_connector

This tool is designed to synchronize the entries in a four-tool system, which includes a - project registration system (eGroupware), - an electronic lab book (Rspace), - an image database (OMERO), - a long-term netstorage system (LINstore)

Language: Python - Size: 5.54 MB - Last synced at: 4 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

ome/omero-mapr

An OMERO.web app allowing to browse the data through attributes linked to the image

Language: Python - Size: 420 KB - Last synced at: 8 days ago - Pushed at: 5 months ago - Stars: 5 - Forks: 13

ome/minimal-omero-client

Language: Java - Size: 114 KB - Last synced at: 8 days ago - Pushed at: 5 months ago - Stars: 1 - Forks: 14

ome/docker-example-omero-grid

Multi-container OMERO

Language: Shell - Size: 52.7 KB - Last synced at: 8 days ago - Pushed at: almost 4 years ago - Stars: 2 - Forks: 12

ome/omero-gallery

Language: JavaScript - Size: 1.4 MB - Last synced at: 8 days ago - Pushed at: 2 months ago - Stars: 5 - Forks: 15

GReD-Clermont/simple-omero-client

Maven project to easily connect to OMERO.

Language: Java - Size: 2.37 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 9 - Forks: 7

ome/omero-upload

OMERO Python library for uploading files

Language: Python - Size: 77.1 KB - Last synced at: 8 days ago - Pushed at: 5 months ago - Stars: 1 - Forks: 4

ome/omero-webtest

An OMERO.web app for prototypes and examples

Language: HTML - Size: 133 KB - Last synced at: 8 days ago - Pushed at: 5 months ago - Stars: 3 - Forks: 12

ome/omero-cli-duplicate

OMERO command-line tool for duplicating database objects

Language: Python - Size: 73.2 KB - Last synced at: 8 days ago - Pushed at: 5 months ago - Stars: 2 - Forks: 8

ome/omero-weberror

An OMERO.web app for generating Web errors

Language: Python - Size: 63.5 KB - Last synced at: 8 days ago - Pushed at: 5 months ago - Stars: 0 - Forks: 9

ome/omero-parade

OMERO.web plugin for displaying Dataset thumbnails or Plates in webclient center panel

Language: JavaScript - Size: 689 KB - Last synced at: 8 days ago - Pushed at: about 1 month ago - Stars: 1 - Forks: 13

ome/omero-dropbox

OMERO.dropbox server for watching directories

Language: Python - Size: 453 KB - Last synced at: 8 days ago - Pushed at: 5 months ago - Stars: 1 - Forks: 6

WU-BIMAC/W-IDM_OmeroImporter

This repository contains software that was developed for the management of bioimage data generated at UMass Chan Medical School and as part of the Canada Bioimaging RDM initiative.

Language: Java - Size: 10.2 MB - Last synced at: 1 day ago - Pushed at: 12 months ago - Stars: 4 - Forks: 1

BiologyTools/BioGTK

A cross platform version of Bio library & program. Bio is a library & program for annotating, & editing various microscopy imaging formats using Bioformats supported images. including whole slide, pyramidal & series.

Language: C# - Size: 146 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 8 - Forks: 2

CBIIT/nife-omero

OMERO instance for microscopy image management in NCI's Imaging Facilities Environment (NIFE).

Language: HTML - Size: 749 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

TheJacksonLaboratory/jax-omeroutils

A module and scripts for working with OMERO

Language: Python - Size: 186 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 6 - Forks: 3

ome/omero-insight

Gradle project containing insight java client for OMERO

Language: Java - Size: 23.7 MB - Last synced at: 1 day ago - Pushed at: 7 months ago - Stars: 7 - Forks: 14

WU-BIMAC/W-IDM_OmeroImporterPy

This repository contains software that was developed to add metadata annotations to bioimage data before importing it into OMERO

Language: Python - Size: 103 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 3 - Forks: 0

TheJacksonLaboratory/omero-training-materials

Repo with materials for OMERO training and scripts to set up a training server.

Language: Python - Size: 23.8 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 2 - Forks: 1

WU-BIMAC/MicroMetaApp-Omero

This is a limited-functionality, beta - implementation of the integration of Micro-Meta App in the OMERO.web client

Language: JavaScript - Size: 27.9 MB - Last synced at: 1 day ago - Pushed at: 8 months ago - Stars: 4 - Forks: 2

ome/omero-docs-superbuild

OMERO build for doc components

Size: 201 KB - Last synced at: 8 days ago - Pushed at: 6 months ago - Stars: 0 - Forks: 1

ome/omero-deployment-examples

Examples playbooks for installing OMERO with Ansible and Docker

Size: 343 KB - Last synced at: 8 days ago - Pushed at: over 1 year ago - Stars: 11 - Forks: 12

hip-satomi/microbeSEG

Deep learning-based instance segmentation tool for roundish objects in 2D and 2D+t data

Language: Python - Size: 8.44 MB - Last synced at: 10 months ago - Pushed at: about 2 years ago - Stars: 7 - Forks: 1

ome/omero-test-infra

Test infrastructure for decoupled repositories

Language: Shell - Size: 153 KB - Last synced at: 8 days ago - Pushed at: 11 months ago - Stars: 3 - Forks: 13

rmassei/2024-jn-omero-pipeline

Material and Instruction for the course "Bioimage data management and analysis with OMERO"

Language: Jupyter Notebook - Size: 32.1 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 2 - Forks: 0

joshmoore/omero-dropbox Fork of ome/omero-dropbox

OMERO.dropbox server for watching directories

Language: Python - Size: 428 KB - Last synced at: 12 months ago - Pushed at: almost 5 years ago - Stars: 0 - Forks: 0

Related Keywords

omero 161 ome 25 python 24 ansible 22 omero-web 19 omero-server 19 docker 18 webapp 12 openmicroscopy 11 role 10 imaging-solutions 9 component 9 deployment 9 omero-import 9 server 8 plugin 7 metadata 7 build 7 java 6 cli 6 annotation-tool 6 microscopy-data 6 bioimaging 6 gradle 6 lib 6 jar 6 microscopy-images 5 jupyter-notebook 5 meta-repo 5 imagej 5 research-data-management 4 omero-web-app 4 bio-formats 4 web 4 idr 4 biomero 3 plugins 3 ice 3 microscopy 3 client 3 qupath 3 jupyter 3 zarr 3 monitoring 3 prometheus 3 command 3 example 3 maven 3 library 3 metadata-management 3 fiji 3 notebook 3 ezomero 3 scripts 3 aws 2 omero-configuration 2 omero-cli-plugin 2 ssh 2 biology 2 omero-cli 2 omero-py 2 roi 2 conda 2 whole-slide-image 2 nfdi4bioimage 2 jupyterhub 2 geojson 2 imagej-macro 2 imagej-roi 2 playbook 2 cell-segmentation 2 matlab 2 docs 2 omero-training 2 deep-learning 2 microbes 2 microservice 2 high-throughput-screening 2 image-analysis 2 omero-scripts 2 slurm 2 io 2 biaflows 2 cytomine 2 jenkins 2 zeroc 2 model 2 fair 2 high-performance-computing 2 image 2 data-management 2 high-content-screening 2 ome-tiff 1 proceedings 1 supplemental-materials 1 whole-slide-imaging 1 human-in-the-loop 1 platform-independent 1 pom 1 html 1

GitHub topics: omero

Cellular-Imaging-Amsterdam-UMC/NL-BIOMERO Fork of ome/docker-example-omero-grid

joshmoore/omero-dropbox Fork of ome/omero-dropbox

joshmoore/ansible-role-omero-web-runtime Fork of ome/ansible-role-omero-web-runtime

GReD-Clermont/omero_batch-plugin Fork of brau-frederic/mica_omero

openmicroscopy/omero-example-scripts Fork of ome/omero-user-scripts