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microscopemetrics-schema

mri-ijlib

A library of ImageJ functions used in tools developped at the MRI imaging facility

mri-workshop-machine-learning

The MRI machine learning workshop

mripy

MRI ImageJ related python (jython) module.

multiscale-spot-detection

Detect spots and their diameters in images containing spots of different sizes.

napari

napari: a fast, interactive, multi-dimensional image viewer for python

napari-bigfish

A napari-plugin providing an alternative GUI for Big-FISH. Big-FISH is a python package for the analysis of smFISH images

napari-blob-detection

napari plugin for blob detection in images

napari-j

Connect Napari with FIJI/ImageJ

napari-surfaces

Tools to work with iso-surfaces and meshes in napari

naparij

neubias

Presentation of the work of NeuBIAS for the image analysis workgroup of MRI

neurite_labelling_ij_plugin

Label neurites with the label of the closest soma with respect to the distance along the paths on the neurites

ome-smuggler

Sneakily imports image goodies into OMERO without paying MRI session duties.

omero-imagej-scripts

omero-python-scripts

Basic and daily use python scripts for interacting with OMERO

omx-t

openmicroscopy

OME (Open Microscopy Environment) develops open-source software and data format standards for the storage and manipulation of biological light microscopy data. A joint project between universities, research establishments and industry in Europe and the USA, OME has over 20 active researchers with strong links to the microscopy community. Funded by private and public research grants, OME has been a major force on the international microscopy stage since 2000.

peakinspector

PeakInspector

point-pattern-analysis

presentations

psf-analysis

Extract psfs and find aberrations like a tilt and a banana shape of the psf-core

python_in_an_hour

A short introduction to python as a supplement to the MRI Machine Learning workshop

qupath_scripts

General qupath scripts that are not project specific

rtd-tutorial

readthedocs tutorial

scripts

Core OMERO Scripts

set-scale-tool

spine-analyzer

The tools allow to semi-automatically segment dendritic spines in 3D+t images and to measure their volumes and the intensities of the signal within in different channels over time.

spots-in-yeasts

Napari plugin producing a segmentation of yeast cells according to their transmission channel, and detecting YFP spots in the fluo channel.

spots-to-membrane

Segment cells in 3D from a membrane staining and process the distance between spots (from a CSV) and the membrane.