TheJacksonLaboratory/ezomero

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

Language: Python - Size: 1.1 MB - Last synced: 6 days ago - Pushed: 6 days ago - Stars: 32 - Forks: 10

ome/omero-server

Gradle project containing main server logic for OMERO

Language: Java - Size: 5.71 MB - Last synced: 20 days ago - Pushed: about 1 month ago - Stars: 4 - Forks: 14

ome/omero-documentation

Sphinx-based documentation for the Open Microscopy Environment

Language: Shell - Size: 233 MB - Last synced: 20 days ago - Pushed: 21 days ago - Stars: 19 - Forks: 50

ome/devspace

Continuous integration tool for OME projects

Language: Shell - Size: 845 KB - Last synced: 20 days ago - Pushed: 20 days ago - Stars: 18 - Forks: 20

ome/omero-plugins

Collection of OMERO extensions (plugins, apps)

Size: 502 KB - Last synced: 20 days ago - Pushed: 20 days ago - Stars: 0 - Forks: 7

ome/omero-guides

Guides for using OMERO

Language: Python - Size: 963 KB - Last synced: 20 days ago - Pushed: about 1 month ago - Stars: 1 - Forks: 5

ome/omero-python-superbuild

OMERO build for Python server components

Size: 380 KB - Last synced: 19 days ago - Pushed: 20 days ago - Stars: 0 - Forks: 4

ome/omero-docs-superbuild

OMERO build for doc components

Size: 195 KB - Last synced: 20 days ago - Pushed: 22 days ago - Stars: 0 - Forks: 1

ome/omero-cli-transfer

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

Language: Python - Size: 3.46 MB - Last synced: 20 days ago - Pushed: 29 days ago - Stars: 12 - Forks: 13

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: about 4 hours ago - Pushed: about 1 month ago - Stars: 2 - Forks: 1

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: 20 days ago - Pushed: 20 days ago - Stars: 2 - Forks: 0

manics/kubernetes-omero

Kubernetes Helm charts for OMERO

Language: Python - Size: 1.44 MB - Last synced: 21 days ago - Pushed: 21 days ago - Stars: 6 - Forks: 10

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: 45.9 KB - Last synced: 22 days ago - Pushed: 22 days ago - Stars: 1 - Forks: 0

tlambert03/napari-omero

Browse your OMERO database from within napari.

Language: Python - Size: 9.66 MB - Last synced: 8 days ago - Pushed: 8 days ago - Stars: 33 - Forks: 10

ome/omero-insight

Gradle project containing insight java client for OMERO

Language: Java - Size: 23.7 MB - Last synced: 20 days ago - Pushed: 29 days ago - Stars: 6 - Forks: 14

WU-BIMAC/W-IDM_OmeroImporterExcelHelperPy

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: Python - Size: 144 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0

ome/omero-gateway-java

Gradle project containing OMERO Java Client Library

Language: Java - Size: 1.19 MB - Last synced: 20 days ago - Pushed: about 1 month ago - Stars: 1 - Forks: 9

ome/omero-blitz

Gradle project containing Ice remoting code for OMERO

Language: Java - Size: 8.85 MB - Last synced: 20 days ago - Pushed: about 1 month ago - Stars: 0 - Forks: 15

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: 3 days ago - Pushed: about 1 month ago - Stars: 8 - Forks: 2

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

OMERO.dropbox server for watching directories

Language: Python - Size: 428 KB - Last synced: about 1 month ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 0

joshmoore/omero-cli-diagnostics

OMERO command-line tool for printing diagnostics

Language: Python - Size: 11.7 KB - Last synced: about 1 month ago - Pushed: almost 7 years ago - Stars: 1 - Forks: 0

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

Language: Python - Size: 9.77 KB - Last synced: about 1 month ago - Pushed: about 7 years ago - Stars: 0 - Forks: 0

rmassei/2024_flowcitometry_multichannel

An integrative workflow to extract single images from flow citometry files and create multichannel ome.tiff images

Language: Jupyter Notebook - Size: 254 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0

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

Language: Java - Size: 2.39 MB - Last synced: about 2 months ago - Pushed: 7 months ago - Stars: 5 - Forks: 0

GReD-Clermont/simple-omero-client

Maven project to easily connect to OMERO.

Language: Java - Size: 2.04 MB - Last synced: about 2 months ago - Pushed: 2 months ago - Stars: 10 - Forks: 7

NFDI4BIOIMAGE/omero-tabbles

OMERO.web script to create Annotations in OMERO based on Tags from Tabbles

Language: Python - Size: 60.5 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 2 - Forks: 0

ome/omero-server-docker

OMERO.server production docker image

Language: Shell - Size: 154 KB - Last synced: about 2 months ago - Pushed: 2 months ago - Stars: 12 - Forks: 24

ome/omero-web-docker

OMERO.web production docker image

Language: Makefile - Size: 133 KB - Last synced: about 2 months ago - Pushed: 3 months ago - Stars: 6 - Forks: 18

ome/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.

Language: Java - Size: 1.85 GB - Last synced: about 2 months ago - Pushed: 2 months ago - Stars: 184 - Forks: 103

ome/omero-model

Gradle project for generating model jar for OMERO

Language: Java - Size: 6.63 MB - Last synced: about 2 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 13

ome/omero-py

Python project containing Ice remoting code for OMERO

Language: Python - Size: 11.5 MB - Last synced: about 2 months ago - Pushed: 2 months ago - Stars: 19 - Forks: 31

ome/omero-figure

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

Language: JavaScript - Size: 7.35 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 13 - Forks: 28

ome/omero-iviewer

An OMERO.web app allowing to view images

Language: JavaScript - Size: 11.9 MB - Last synced: about 2 months ago - Pushed: 2 months ago - Stars: 17 - Forks: 27

ome/omero-common

Gradle project containing common utilities for OMERO

Language: Java - Size: 1.72 MB - Last synced: about 2 months ago - Pushed: 3 months ago - Stars: 1 - Forks: 11

ome/omero-cli-render

OMERO command-line tool for rendering

Language: Python - Size: 407 KB - Last synced: about 2 months ago - Pushed: 3 months ago - Stars: 2 - Forks: 10

ome/omero-build

OMERO top-level build for all components

Language: Dockerfile - Size: 396 KB - Last synced: about 2 months ago - Pushed: 3 months ago - Stars: 1 - Forks: 7

ome/omero-scripts

Core OMERO Scripts

Language: Python - Size: 1.61 MB - Last synced: about 2 months ago - Pushed: 2 months ago - Stars: 11 - Forks: 31

ome/minimal-omero-client

Language: Java - Size: 109 KB - Last synced: about 2 months ago - Pushed: 3 months ago - Stars: 1 - Forks: 14

ome/ansible-role-omero-web

Installs and configures OMERO.web and Nginx

Language: Python - Size: 178 KB - Last synced: about 2 months ago - Pushed: 2 months ago - Stars: 1 - Forks: 14

ome/omero-metadata

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

Language: Python - Size: 462 KB - Last synced: about 2 months ago - Pushed: 3 months ago - Stars: 7 - Forks: 13

TheJacksonLaboratory/jax-omeroutils

A module and scripts for working with OMERO

Language: Python - Size: 153 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 6 - Forks: 3

ome/omero-cli-duplicate

OMERO command-line tool for duplicating database objects

Language: Python - Size: 70.3 KB - Last synced: about 2 months ago - Pushed: 3 months ago - Stars: 2 - Forks: 8

ome/ansible-role-omero-web-django-prometheus

Django Prometheus Exporter for OMERO.web

Language: Jinja - Size: 39.1 KB - Last synced: about 2 months ago - Pushed: 4 months ago - Stars: 1 - Forks: 6

ome/omero-certificates

OMERO server certificate management plugin

Language: Python - Size: 104 KB - Last synced: about 2 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 7

ome/omero-web

Django-based OMERO.web client

Language: Python - Size: 24.9 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 14 - Forks: 28

ome/omero-rois

OMERO python ROI utils

Language: Python - Size: 73.2 KB - Last synced: about 2 months ago - Pushed: 3 months ago - Stars: 2 - Forks: 4

ome/omero-dropbox

OMERO.dropbox server for watching directories

Language: Python - Size: 457 KB - Last synced: about 2 months ago - Pushed: 3 months ago - Stars: 1 - Forks: 6

ome/omero-upload

OMERO Python library for uploading files

Language: Python - Size: 82 KB - Last synced: about 2 months ago - Pushed: 3 months ago - Stars: 1 - Forks: 4

ome/ansible-role-omero-common

Common variables and tasks for OME applications

Language: Python - Size: 27.3 KB - Last synced: about 2 months ago - Pushed: 3 months ago - Stars: 1 - Forks: 6

ome/docker-example-omero

OMERO Docker compose example

Language: Shell - Size: 21.5 KB - Last synced: about 2 months ago - Pushed: 4 months ago - Stars: 21 - Forks: 26

ome/omero-guide-cellprofiler

Language: Jupyter Notebook - Size: 1.77 MB - Last synced: 20 days ago - Pushed: about 2 months ago - Stars: 4 - Forks: 4

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

Multi-container OMERO with BIOMERO for AMC

Language: CSS - Size: 11.5 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 3 - Forks: 1

sorgerlab/omero-nginx-docker

Nginx docker image for OMERO.web

Language: Shell - Size: 3.91 KB - Last synced: 3 months ago - Pushed: over 6 years ago - Stars: 0 - Forks: 4

sorgerlab/omero.cloudarchive-docker

OMERO Cloudarchive Docker

Language: Python - Size: 28.3 KB - Last synced: 3 months ago - Pushed: over 6 years ago - Stars: 0 - Forks: 2

sorgerlab/omero-ms-pixel-buffer-docker

Docker image for pixel-buffer OMERO microservice

Language: Shell - Size: 1.95 KB - Last synced: 3 months ago - Pushed: almost 7 years ago - Stars: 0 - Forks: 0

sorgerlab/omero.cloudarchive-cloudformation

OMERO Cloudarchive Cloudformation

Language: Shell - Size: 24.4 KB - Last synced: 3 months ago - Pushed: over 6 years ago - Stars: 1 - Forks: 1

sorgerlab/OMERO.forms

Extension to OMERO.web to enhance metadata input and provide provenance

Language: Python - Size: 1.66 MB - Last synced: about 2 months ago - Pushed: 6 months ago - Stars: 7 - Forks: 4

NL-BioImaging/biomero-scripts

Scripts for use with BIOMERO / the Omero Slurm Client library

Language: Python - Size: 76.2 KB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 0 - Forks: 0

NL-BioImaging/biomero

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

Language: Python - Size: 4.4 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 7 - Forks: 0

ome/omero-ssh-daemon-docker

Docker image for testing OMERO on Rocky Linux 9.

Language: Dockerfile - Size: 13.7 KB - Last synced: about 2 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 3

ome/ansible-role-omero-logmonitor

Install OmeroFenton for error notifications in Jabber

Language: Jinja - Size: 42 KB - Last synced: about 2 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 5

ome/omero-cli-zarr

Language: Python - Size: 343 KB - Last synced: about 2 months ago - Pushed: 2 months ago - Stars: 15 - Forks: 10

ome/ansible-role-hosts-populate

Populates /etc/hosts with static addresses for a list of hostgroups

Language: Python - Size: 27.3 KB - Last synced: about 2 months ago - Pushed: 4 months ago - Stars: 1 - Forks: 5

ome/ansible-role-reboot-server

Reboot a server, optionally wait for it to return

Language: Python - Size: 22.5 KB - Last synced: about 2 months ago - Pushed: 4 months ago - Stars: 1 - Forks: 6

imcf/hrm-omero

The HRM-OMERO connector

Language: Python - Size: 497 KB - Last synced: 1 day ago - Pushed: over 1 year ago - Stars: 3 - Forks: 0

ome/ansible-role-omero-user

Create OMERO user accounts and groups

Language: Python - Size: 29.3 KB - Last synced: about 2 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 5

ome/omero-gallery

Language: JavaScript - Size: 1.34 MB - Last synced: about 2 months ago - Pushed: 11 months ago - Stars: 5 - Forks: 14

arkitektio/omero-ark-server

An OMERO proxy server hosting a GraphQL API

Language: Python - Size: 307 KB - Last synced: about 1 month ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

ome/rOMERO-gateway

OMERO R Gateway

Language: R - Size: 375 KB - Last synced: 20 days ago - Pushed: 7 months ago - Stars: 5 - Forks: 10

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

Plugins for OMERO

Language: Python - Size: 221 KB - Last synced: 3 months ago - Pushed: over 6 years ago - Stars: 9 - Forks: 5

ome/ansible-role-omero-server

Installs and configures OMERO.server

Language: Python - Size: 263 KB - Last synced: about 2 months ago - Pushed: 3 months ago - Stars: 4 - Forks: 14

ome/omero-deployment-examples

Examples playbooks for installing OMERO with Ansible and Docker

Size: 343 KB - Last synced: about 2 months ago - Pushed: 11 months ago - Stars: 9 - Forks: 12

TheJacksonLaboratory/omero_for_developers

material for the "OMERO for developers" workshop.

Language: Jupyter Notebook - Size: 32.2 KB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 2 - Forks: 2

ome/omero-downloader

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

Language: Java - Size: 322 KB - Last synced: about 2 months ago - Pushed: 11 months ago - Stars: 3 - Forks: 5

ome/omero-ms-zarr

Experimental micro-service for implementing the Zarr spec over HTTP

Language: Java - Size: 354 KB - Last synced: 20 days ago - Pushed: about 1 month ago - Stars: 16 - Forks: 12

GReD-Clermont/omero_macro-extensions

Language: Java - Size: 212 KB - Last synced: about 2 months ago - Pushed: 2 months ago - Stars: 6 - Forks: 5

German-BioImaging/webtagging 📦

Extensions to OMERO.web to enhance tagging and searching

Language: JavaScript - Size: 1.21 MB - Last synced: 8 months ago - Pushed: 12 months ago - Stars: 4 - Forks: 6

ome/ansible-example-omero-onenode

Example of deploying an OMERO.server on a single-node

Language: Python - Size: 33.2 KB - Last synced: about 2 months ago - Pushed: 11 months ago - Stars: 1 - Forks: 7

ome/ecdp2019-publication

Supplementary information associated with Besson et al. (2019) ECDP 2019

Language: Python - Size: 6.43 MB - Last synced: about 2 months ago - Pushed: over 3 years ago - Stars: 2 - Forks: 3

ome/omero-test-infra

Test infrastructure for decoupled repositories

Language: Shell - Size: 149 KB - Last synced: about 2 months ago - Pushed: 4 months ago - Stars: 3 - Forks: 14

ome/omero-weberror

An OMERO.web app for generating Web errors

Language: Python - Size: 59.6 KB - Last synced: about 2 months ago - Pushed: 12 months ago - Stars: 0 - Forks: 9

WU-BIMAC/W-IDM_OmeroDataWriter

This repository contains sofware that was created for the automatic image data management of image data generated at UMass Chan Medical School and as part of the Canada Bioimaging RDM initiative.

Language: Java - Size: 43.9 KB - Last synced: about 5 hours ago - Pushed: almost 2 years ago - Stars: 2 - Forks: 0

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: about 3 hours ago - Pushed: about 1 year ago - Stars: 3 - Forks: 1

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: over 1 year ago - Pushed: over 1 year ago - Stars: 6 - Forks: 0

hip-satomi/ObiWan-Microbi

Omero based integrated Workflow for annotating Microbes in the Cloud

Language: Dockerfile - Size: 12.4 MB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 4 - Forks: 1

ome/omero_searcher 📦

Language: Python - Size: 702 KB - Last synced: about 2 months ago - Pushed: over 10 years ago - Stars: 1 - Forks: 4

ome/webemdb 📦

OMERO.web EMDB

Language: Python - Size: 2.62 MB - Last synced: about 2 months ago - Pushed: over 12 years ago - Stars: 2 - Forks: 2

ome/ansible-role-devspace 📦

Provision OME developer devspace

Size: 43 KB - Last synced: about 2 months ago - Pushed: over 3 years ago - Stars: 0 - Forks: 8

ome/ansible-role-omero-web-runtime 📦

DEPRECATED: please see https://github.com/openmicroscopy/ansible-role-omero-python-deps

Language: Python - Size: 12.7 KB - Last synced: about 2 months ago - Pushed: over 3 years ago - Stars: 0 - Forks: 4

ome/pom-omero-client 📦

Parent POM for OMERO clients (deprecated)

Size: 54.7 KB - Last synced: about 2 months ago - Pushed: over 3 years ago - Stars: 1 - Forks: 5

ome/ome-release 📦

Scripts for OME releases (deprecated)

Language: HTML - Size: 3.1 MB - Last synced: about 2 months ago - Pushed: over 3 years ago - Stars: 0 - Forks: 11

ome/ansible-role-omero-web-apps 📦

Install OMERO.web plugins. **DEPRECATED**: use github.com/ome/ansible-role-omero-web

Language: Python - Size: 31.3 KB - Last synced: about 2 months ago - Pushed: over 3 years ago - Stars: 1 - Forks: 6

ome/ansible-role-omego 📦

omego, a utility for downloading and installing OME applications

Language: HTML - Size: 20.5 KB - Last synced: about 2 months ago - Pushed: over 3 years ago - Stars: 0 - Forks: 5

ome/ansible-role-omero-python-deps 📦

Install Python dependencies for OMERO.

Language: HTML - Size: 21.5 KB - Last synced: about 2 months ago - Pushed: over 3 years ago - Stars: 0 - Forks: 6

ome/conda-omero-py 📦

OMERO.py Conda package

Size: 49.8 KB - Last synced: about 2 months ago - Pushed: about 2 years ago - Stars: 0 - Forks: 5

ome/conda-zeroc-ice36-python 📦

Zeroc Ice Python Conda package for OMERO

Size: 68.4 KB - Last synced: about 2 months ago - Pushed: about 2 years ago - Stars: 0 - Forks: 2

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: about 1 year ago - Pushed: over 1 year ago - Stars: 4 - Forks: 1

ome/omero-parade

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

Language: JavaScript - Size: 657 KB - Last synced: 20 days ago - Pushed: 7 months ago - Stars: 1 - Forks: 12

ome/omero-install

OMERO installation scripts

Language: Shell - Size: 1.11 MB - Last synced: about 2 months ago - Pushed: 4 months ago - Stars: 4 - Forks: 24

ome/prod-playbooks

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

Language: Python - Size: 1.28 MB - Last synced: 20 days ago - Pushed: 7 months ago - Stars: 4 - Forks: 19