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    73 repositories

    • open-desks-app

      Public
      Booking application used by MRI-CIA for the open-desk sessions.
      PHP
      •0•0•0•0•Updated Feb 26, 2025Feb 26, 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 Feb 21, 2025Feb 21, 2025

    • microscopemetrics-schema

      Public
      Python
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Feb 14, 2025Feb 14, 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 Feb 13, 2025Feb 13, 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
      •16•33•3•0•Updated Feb 12, 2025Feb 12, 2025

    • UNETR_2D_Tree_Rings

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

    • entry-exit-mouse-box

      Public
      Python
      •
      MIT License
      •0•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

    • 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 Jan 16, 2025Jan 16, 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•13•2•0•Updated Jan 13, 2025Jan 13, 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•1•0•Updated Jan 10, 2025Jan 10, 2025

    • qupath_multiplex_analysis

      Public
      Tools to facilitate multiplex image analysis with QuPath
      Groovy
      •
      MIT License
      •0•0•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

    • microscope-metrics

      Public
      Python
      •
      MIT License
      •6•0•13•4•Updated Nov 26, 2024Nov 26, 2024

    • mri-cia-documents

      Public
      Public documents related to the MRI-CIA service.
      0•0•0•0•Updated Nov 20, 2024Nov 20, 2024

    • presentations

      Public
      HTML
      •0•0•0•0•Updated Nov 12, 2024Nov 12, 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

    • qupath_scripts

      Public
      General qupath scripts that are not project specific
      Groovy
      •
      MIT License
      •0•0•0•0•Updated Oct 30, 2024Oct 30, 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

    • napari-J

      Public
      Connect Napari with FIJI/ImageJ
      imagejfijiimage-analysisbioimage-analysisnapari-pluginpython
      Python
      •
      MIT License
      •2•2•1•0•Updated Aug 7, 2024Aug 7, 2024

    • mri-workshop-machine-learning

      Public
      The MRI machine learning workshop
      machine-learningdeep-learningconvolutional-neural-networksworkshop-materials
      Jupyter Notebook
      •1•3•0•0•Updated May 23, 2024May 23, 2024

    • meiosis_bar

      Public
      ImageJ Macro
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Apr 26, 2024Apr 26, 2024

    • spots-to-membrane

      Public
      Segment cells in 3D from a membrane staining and process the distance between spots (from a CSV) and the membrane.
      Python
      •
      MIT License
      •0•0•0•0•Updated Apr 2, 2024Apr 2, 2024

    • microscopemetrics-dashboard

      Public
      Python
      •
      GNU General Public License v2.0
      •2•0•0•0•Updated Jan 23, 2024Jan 23, 2024

    • microscopemetrics-omero

      Public
      Python
      •
      GNU General Public License v2.0
      •2•1•0•0•Updated Jan 11, 2024Jan 11, 2024

    • psf-analysis

      Public
      Extract psfs and find aberrations like a tilt and a banana shape of the psf-core
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Dec 22, 2023Dec 22, 2023

    • set-scale-tool

      Public
      Python
      •
      MIT License
      •0•1•0•0•Updated Nov 3, 2023Nov 3, 2023

    • dl4mic

      Public
      Project to deploy the ZeroCostDL4Mic networks to the users of the facility. Run the training and application of the networks as python scripts.
      Jupyter Notebook
      •1•1•0•0•Updated Jul 19, 2023Jul 19, 2023