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    80 repositories

    • Spatial_Heterogeneity_Of_Transcription

      Public
      Analyze the spatial heterogeneity of transcription
      Python
      •
      MIT License
      •0•0•0•0•Updated Aug 1, 2025Aug 1, 2025

    • napari-sphot

      Public
      A napari plugin to analyze the spatial heterogenity of transcription witin the cells of an embryo.
      Python
      •
      MIT License
      •0•0•0•0•Updated Aug 1, 2025Aug 1, 2025

    • set-scale-tool

      Public
      Python
      •
      MIT License
      •0•1•0•0•Updated Aug 1, 2025Aug 1, 2025

    • napari-tree-rings

      Public
      A napari plugin to delineate bark, pith, and xylem annual rings and to measure their area and thickness on circular sections of a tree trunk.
      Python
      •
      MIT License
      •0•0•0•0•Updated Jul 28, 2025Jul 28, 2025

    • tree-ring-analyzer

      Public
      Segment tree rings and analyze them.
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jul 25, 2025Jul 25, 2025

    • imagej_macros_and_scripts

      Public
      ImageJ macros and scripts written at the imaging facility MRI
      imagejfijiimagej-pluginsjythonimage-analysis-workflowsimagej-macrobioimage-analysisfiji-macrotoolsetsimagej-macro-scripts
      Jupyter Notebook
      •
      MIT License
      •18•35•4•0•Updated Jul 24, 2025Jul 24, 2025

    • napari-bigfish

      Public
      A napari-plugin providing an alternative GUI for Big-FISH. Big-FISH is a python package for the analysis of smFISH images
      Python
      •
      MIT License
      •1•3•1•0•Updated Jul 23, 2025Jul 23, 2025

    • bacteria-density

      Public
      Python
      •0•0•0•0•Updated Jul 18, 2025Jul 18, 2025

    • mri-cia-documents

      Public
      Public documents related to the MRI-CIA service.
      0•0•0•0•Updated Jun 27, 2025Jun 27, 2025

    • 3D-synthetic-spots-in-cells

      Public
      Create 3D ground truth data of different spot distributions in cells
      Python
      •
      MIT License
      •0•0•0•0•Updated Jun 19, 2025Jun 19, 2025

    • basics-of-python

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Jun 11, 2025Jun 11, 2025

    • mri-workshop-machine-learning

      Public
      The MRI machine learning workshop
      machine-learningdeep-learningconvolutional-neural-networksworkshop-materials
      Jupyter Notebook
      •1•3•0•0•Updated Jun 6, 2025Jun 6, 2025

    • microscope-metrics

      Public
      Python
      •
      MIT License
      •6•0•13•4•Updated Jun 4, 2025Jun 4, 2025

    • microscopemetrics-schema

      Public
      Python
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated May 26, 2025May 26, 2025

    • entry-exit-mouse-box

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated May 22, 2025May 22, 2025

    • microglia-analyzer

      Public
      A Napari plugin meant to detect and segment microglia before extracting some measures about them.
      Python
      •
      MIT License
      •0•2•0•0•Updated May 20, 2025May 20, 2025

    • OMERO-metrics

      Public
      OMERO-metrics is an omero web app to analyze and visualize microscope metrology data
      omeroomero-web-appomero-metrics
      Python
      •
      GNU Affero General Public License v3.0
      •3•1•2•0•Updated May 16, 2025May 16, 2025

    • qupath_scripts

      Public
      General qupath scripts that are not project specific
      Groovy
      •
      MIT License
      •0•0•0•0•Updated Apr 10, 2025Apr 10, 2025

    • presentations

      Public
      HTML
      •0•0•0•0•Updated Apr 8, 2025Apr 8, 2025

    • open-desks-app

      Public
      Booking application used by MRI-CIA for the open-desk sessions.
      PHP
      •1•2•0•0•Updated Apr 6, 2025Apr 6, 2025

    • MRI-CIA

      Public
      Overview of the tools, scripts and workshops created by the image analysis service of the Montpellier Ressources Imagerie imaging facility.
      MIT License
      •0•0•0•0•Updated Mar 12, 2025Mar 12, 2025

    • UNETR_2D_Tree_Rings

      Public
      2D UNETR implementation in Tensorflow-keras, for the segmentation of annual tree rings.
      Jupyter Notebook
      •
      MIT License
      •3•0•0•0•Updated Feb 10, 2025Feb 10, 2025

    • horizontal-growth-of-trees

      Public
      A tool to delineate bark, pith, and xylem annual rings and to measure their area and thickness on circular sections of a tree trunk.
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Feb 3, 2025Feb 3, 2025

    • segment-embryo

      Public
      Segment the cells of an ascidian embryon, detect the stained mRNA molecules per cell and analyze their distribution
      Python
      •
      MIT License
      •0•0•0•0•Updated Jan 15, 2025Jan 15, 2025

    • MetroloJ_QC

      Public
      Java
      •1•15•3•0•Updated Jan 13, 2025Jan 13, 2025

    • qupath_multiplex_analysis

      Public
      Tools to facilitate multiplex image analysis with QuPath
      Groovy
      •
      MIT License
      •0•1•0•0•Updated Jan 7, 2025Jan 7, 2025

    • spots-in-yeasts

      Public
      Napari plugin producing a segmentation of yeast cells according to their transmission channel, and detecting YFP spots in the fluo channel.
      Python
      •
      MIT License
      •0•0•0•0•Updated Nov 27, 2024Nov 27, 2024

    • i2k-2024-meshes

      Public
      Python
      •2•0•0•0•Updated Nov 12, 2024Nov 12, 2024

    • point-pattern-analysis

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Nov 12, 2024Nov 12, 2024

    • 3D-Image-Analysis-Workshop

      Public
      Workshop material for the 3D image analysis workshop
      TeX
      •
      MIT License
      •0•0•0•0•Updated Oct 7, 2024Oct 7, 2024