Ecosyste.ms: Repos

An open API service providing repository metadata for many open source software ecosystems.

GitHub topics: microscopy-data

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: 2 days ago - Pushed: 26 days ago - Stars: 2 - Forks: 1

tlnagy/Nagy_2023_SwellMigration

Code used to generate the figures for the "Neutrophils Actively Swell to Potentiate Migration" paper

Language: Julia - Size: 32.6 MB - Last synced: 7 days ago - Pushed: 8 days ago - Stars: 0 - Forks: 0

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: 9 days ago - Pushed: 9 days ago - Stars: 1 - Forks: 0

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: 18 days ago - Pushed: 19 days ago - Stars: 0 - Forks: 0

WU-BIMAC/MicroMetaApp-React

This is the React implementation of Micro-Meta App, Microscopy Metadata for the real world!

Language: JavaScript - Size: 30.5 MB - Last synced: 2 days ago - Pushed: 10 months ago - Stars: 6 - Forks: 1

melchisedech333/laser-scanning-microscopy

🧪 Reproducing the concept of Confocal Laser Scanning Microscope. Using Arduino and easily found materials. Generating images in Grayscale just for fun.

Language: PHP - Size: 4.39 MB - Last synced: 28 days ago - Pushed: over 1 year ago - Stars: 4 - Forks: 1

Jack-Gregory-Bioinformatics/ImageJ_Microscopy_Automation

Repository for an automated microscopy image analysis pipeline, using ImageJ.

Language: R - Size: 92.8 KB - Last synced: 3 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

dmattek/dzPlateViewer

Deep Zoom Plate Viewer for microscopy images

Language: JavaScript - Size: 10 MB - Last synced: 7 days ago - Pushed: over 1 year ago - Stars: 15 - Forks: 2

arkitektio-apps/mikro-napari

napari within the mikro environment

Language: Python - Size: 1.04 MB - Last synced: 16 days ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

ElisabethKugler/ZFVascularQuantification

#ZVQ - Zebrafish Vascular Quantification - https://doi.org/10.1242/dev.199720

Language: ImageJ Macro - Size: 3.14 MB - Last synced: 21 days ago - Pushed: about 1 year ago - Stars: 10 - Forks: 0

clintyr/bio-image-analysis

Example workflows for image processing, segmentation and analysis. Stitching and alignment functions also implemented.

Language: Jupyter Notebook - Size: 47.2 MB - Last synced: 4 months ago - Pushed: 7 months ago - Stars: 1 - Forks: 0

georgeglidden/relenc

convolutional-relational neural network architectures for segmentation of electron micrographs

Language: Python - Size: 21.5 KB - Last synced: 7 months ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

sanger-matteo/Analyse-Cell-Colonization-Patterns

Quantify the colonization behaviours on surfaces for different bacterial strains

Language: Mathematica - Size: 90.2 MB - Last synced: 7 months ago - Pushed: about 3 years ago - Stars: 0 - Forks: 0

WU-BIMAC/4DNMetadataSchemaXSD2JSONConverter

This is a converter written in Java that translates an XSD microscopy metadata schema into JSON

Language: Java - Size: 24.9 MB - Last synced: 2 days ago - Pushed: almost 2 years ago - Stars: 3 - Forks: 0

WU-BIMAC/NBOMicroscopyMetadataSpecs

The 4DN + BINA Tiered System of Microscopy Metadata Guidelines was developed by the 4DN Imaging Standards Working Group in collaboration with the BINA Data Management and Quality Control Working Group (https://www.bioimagingna.org/qc-dm-wg) for documenting microscopy experiments and assessing the quality of image data.

Size: 416 MB - Last synced: 2 days ago - Pushed: 11 months ago - Stars: 14 - Forks: 4

Gianluca-G98/Train_microglial_models

The code provides an easy way to train Deep learning models on personal data after logging it on Weights&Biases. It already contains 4 high-performing architectures and allows the user to create and use any desired model.

Language: Python - Size: 3.67 MB - Last synced: 12 months ago - Pushed: over 1 year ago - Stars: 2 - Forks: 0

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: 2 days 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: 2 days ago - Pushed: about 1 year ago - Stars: 3 - Forks: 1

WU-BIMAC/MicroMetaApp-Electron

Electron wrapped, stand-alone version of Micro-Meta App, microscopy metadata for the real world!

Language: JavaScript - Size: 62.6 MB - Last synced: 2 days ago - Pushed: 9 months ago - Stars: 7 - Forks: 0

WU-BIMAC/NBO-Q_MicroscopyGlossary

4DN-BINA-OME-QUAREP Microscopy Glossary

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

ElisabethKugler/GliaMorph

#GliaMorph - Toolkit to Process and Analyse Müller Glia Morphology

Language: ImageJ Macro - Size: 166 KB - Last synced: 15 days ago - Pushed: 6 months ago - Stars: 4 - Forks: 0

FabrizioMusacchio/ZARR_tests

Python code that I used in my blog posts on the Zarr file format.

Language: Python - Size: 4.98 MB - Last synced: 4 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

GVS-Lab/chrometrics

Nuclear Morphology and Chromatin Organization Features

Language: Jupyter Notebook - Size: 4.29 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 2 - Forks: 3

Oftatkofta/cellocity

Scientific software for analysis of confluent cell dynamics.

Language: Python - Size: 69.4 MB - Last synced: 2 days ago - Pushed: 10 months ago - Stars: 6 - Forks: 3

Related Keywords
microscopy-data 24 metadata 10 microscopy-images 8 research-data-management 8 microscopy 7 omero 6 reproducibility 6 metadata-management 6 annotation-tool 5 omero-import 4 microscopy-metadata 4 metadata-standard 3 segmentation 3 omero-web 3 metadata-editor 3 metadata-extraction 3 reporting-tool 3 reporting 3 zebrafish 2 research-data 2 quantification 2 openscience 2 fiji-macro-language 2 fiji 2 napari 2 automation 2 omero-server 2 vector-analysis 1 unet-image-segmentation 1 tensorflow2 1 microglial-morphology 1 machine-learning 1 deep-learning 1 cell-counting 1 dataset 1 model 1 image-analysis-and-processing 1 julia 1 reproducible-paper 1 json-schema 1 microbiology 1 mathematica 1 relational-model 1 relational-encoder 1 encoder-decoder-model 1 convolutional-neural-networks 1 time-series-analysis 1 cell-dynamics 1 analysis 1 texture 1 nucleus 1 morphological-analysis 1 image-features 1 feature-extraction 1 computer-vision 1 zarr 1 python 1 ome-zarr 1 ome 1 bioimaging 1 bioimage-analysis 1 opensource 1 glia 1 fiji-macro 1 comparability 1 confocal-images 1 image-viewer 1 drug-screen 1 deepzoom 1 bioinformatics-pipeline 1 bioinformatics 1 confocal-microscope 1 microscopy-image 1 confocal-microscopy 1 microscopic-images 1 microscopes 1 microscope-images 1 microscope-image 1 microscope-hardware 1 microscope-control 1 microscope 1 laser-scanning 1 laser-scanner 1 image-generation 1 cnn 1 skimage 1 scikit-learn 1 opencv 1 image-segmentation 1 image-processing-python 1 image-analysis 1 cellpose 1 cell-segmentation 1 reproducible-research 1 vasculature 1 registration 1 annotation 1 arduino 1 lightsheet 1 image-processing 1