Deep Zoom Plate Viewer for microscopy images
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Apr 9, 2025 - JavaScript
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microscopy-data
Here are 27 public repositories matching this topic...
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.
metadata model reporting research-data-management reproducibility microscopy metadata-standard research-data microscopy-data microscopy-metadata
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Jun 20, 2023
#ZVQ - Zebrafish Vascular Quantification - https://doi.org/10.1242/dev.199720
fiji image-processing registration segmentation quantification openscience microscopy zebrafish lightsheet microscopy-data vasculature fiji-macro-language
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May 24, 2023 - ImageJ Macro
This is the React implementation of Micro-Meta App, Microscopy Metadata for the real world!
metadata research-data-management reproducibility metadata-editor metadata-extraction metadata-management reporting-tool microscopy-data
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Apr 26, 2025 - JavaScript
Electron wrapped, stand-alone version of Micro-Meta App, microscopy metadata for the real world!
metadata research-data-management reproducibility metadata-editor metadata-extraction metadata-management reporting-tool microscopy-data microscopy-metadata
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Mar 16, 2025 - JavaScript
Scientific software for analysis of confluent cell dynamics.
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Apr 14, 2025 - Python
This repository contains software that was developed to add metadata annotations to bioimage data before importing it into OMERO
metadata research-data-management omero annotation-tool metadata-management omero-server omero-web microscopy-images microscopy-data omero-import
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Dec 3, 2024 - Python
#GliaMorph - Toolkit to Process and Analyse Müller Glia Morphology
opensource fiji segmentation quantification openscience microscopy glia zebrafish fiji-macro comparability microscopy-data fiji-macro-language
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Dec 15, 2023 - ImageJ Macro
🧪 Reproducing the concept of Confocal Laser Scanning Microscope. Using Arduino and easily found materials. Generating images in Grayscale just for fun.
arduino image-generation confocal-microscope arduino-uno microscopy laser-scanner microscope microscopes confocal-microscopy microscopy-images laser-scanning microscope-images microscopic-images confocal microscope-image microscopy-image confocal-images microscope-control microscopy-data microscope-hardware
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Oct 17, 2022 - PHP
Nuclear Morphology and Chromatin Organization Features
computer-vision texture feature-extraction nucleus morphological-analysis microscopy-data image-features
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Feb 15, 2024 - Jupyter Notebook
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.
metadata research-data-management omero annotation-tool microscopy-images microscopy-data omero-import
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May 3, 2024 - Java
This is a limited-functionality, beta - implementation of the integration of Micro-Meta App in the OMERO.web client
metadata reproducibility omero metadata-editor metadata-extraction annotation-tool metadata-management omero-web reporting-tool microscopy-data microscopy-metadata
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Aug 21, 2024 - JavaScript
This is a converter written in Java that translates an XSD microscopy metadata schema into JSON
metadata json-schema reporting reproducibility metadata-standard metadata-management microscopy-data
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Aug 11, 2022 - Java
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.
metadata research-data-management omero annotation-tool microscopy-images microscopy-data omero-import
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Jul 21, 2022 - Java
Repository for an automated microscopy image analysis pipeline (CryptoClassifier), using ImageJ.
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Aug 7, 2024 - R
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.
metadata annotation research-data-management omero annotation-tool metadata-management omero-server omero-web microscopy-images microscopy-data omero-import
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Mar 31, 2025 - Python
Example workflows for image processing, segmentation and analysis. Stitching and alignment functions also implemented.
opencv scikit-learn image-segmentation image-analysis cell-segmentation skimage image-processing-python napari microscopy-data cellpose
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Nov 15, 2023 - Jupyter Notebook
NFDI4BIOIMAGE data management illustrations by Henning Falk (2024)
data-management image-analysis data-reuse bioimaging nfdi microscopy-data microscopy-metadata nfdi4bioimage
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Nov 29, 2024
napari within the mikro environment
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Jun 30, 2024 - Python
Python code that I used in my blog posts on the Zarr file format.
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Oct 24, 2022 - Python
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