Montpellier Ressources Imagerie

All

72 repositories

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 18, 2025Feb 18, 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
imagej fiji imagej-plugins jython image-analysis-workflows imagej-macro bioimage-analysis fiji-macro toolsets imagej-macro-scripts
Jupyter Notebook
•
MIT License
•16•32•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
omero omero-web-app omero-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
imagej fiji image-analysis bioimage-analysis napari-plugin python
Python
•
MIT License
•2•2•1•0•Updated Aug 7, 2024Aug 7, 2024
mri-workshop-machine-learning
Public
The MRI machine learning workshop
machine-learning deep-learning convolutional-neural-networks workshop-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
ij-macro-programming-workshop
Public
The MRI workshop about ImageJ macro programming.
programming imagej macros imagej-macro fiji-macro workshop imagej-macro-programming mri-workshop
TeX
•
MIT License
•1•0•0•0•Updated May 22, 2023May 22, 2023