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    86 repositories

    • napari-tree-rings

      Public
      A napari plugin to delineate bark, pith, and xylem annual rings and to measure their property parameters on circular sections of tree trunks.
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 24, 2025Oct 24, 2025

    • imagej_macros_and_scripts

      Public
      ImageJ macros and scripts written at the imaging facility MRI
      imagejfijiimagej-pluginsjythonimage-analysis-workflowsimagej-macrobioimage-analysisfiji-macrotoolsetsimagej-macros
      Jupyter Notebook
      •
      MIT License
      •18•37•5•0•Updated Oct 24, 2025Oct 24, 2025

    • bacteria-density

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

    • tree-ring-analyzer

      Public
      Segment tree rings and analyze them.
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Oct 22, 2025Oct 22, 2025

    • napari-membrane-intensity

      Public
      Allows to segment cells, track them over time, and measure the intensity in their membrane. For yeasts specifically, also allows to merge each bud with its mother.
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 20, 2025Oct 20, 2025

    • auto-options-python

      Public
      Mange command options in python and create QWidgets for them.
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 19, 2025Oct 19, 2025

    • napari-unet

      Public
      A Napari plugin allowing to make patches from images, train a UNet, run the inference on images and compute metrics. Specially made for filaments.
      Python
      •
      MIT License
      •1•1•0•0•Updated Oct 13, 2025Oct 13, 2025

    • filament-toolbox

      Public
      Tools useful for segmenting and analyzing filaments.
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 12, 2025Oct 12, 2025

    • mifobio2025-meshes

      Public
      Flash tuto about using meshes and Blender in the analysis workflow
      Python
      •0•0•0•0•Updated Oct 6, 2025Oct 6, 2025

    • Workshop-Filament-Analysis

      Public
      A workshop about the specifics of the segmentation and analysis of filaments.
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Sep 23, 2025Sep 23, 2025

    • napari-tracing

      Public
      A Napari plugin to perform brightest path tracing.
      Python
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Sep 18, 2025Sep 18, 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 Sep 16, 2025Sep 16, 2025

    • Spatial_Heterogeneity_Of_Transcription

      Public
      Analyze the spatial heterogeneity of transcription
      Python
      •
      MIT License
      •0•0•0•0•Updated Sep 15, 2025Sep 15, 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
      •4•1•7•0•Updated Sep 8, 2025Sep 8, 2025

    • microscope-metrics

      Public
      Python
      •
      MIT License
      •6•0•13•4•Updated Aug 26, 2025Aug 26, 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 Aug 19, 2025Aug 19, 2025

    • microscopemetrics-omero

      Public
      Python
      •
      GNU General Public License v2.0
      •2•1•0•0•Updated Aug 18, 2025Aug 18, 2025

    • set-scale-tool

      Public
      Python
      •
      MIT License
      •0•1•0•0•Updated Aug 1, 2025Aug 1, 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•4•1•0•Updated Jul 23, 2025Jul 23, 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

    • 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

    • 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