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qupath-extension-cellpose
an extension that wraps a Cellpose environment such that WSI can be analyzed using Cellpose through QuPath.ijp-imagetoatlas
2D sections to 3D atlas registration with Fiji and QuPathijl-utilities-wrappers
Wrappers for external software calls (Cellpose, Elastix, Ilastix...) and java utilities (object conversions and display)IPA4LSx
ImageJ Macro Scripts showcased during Image Processing and Analysis for Life Scientists MOOC on EdXqupath-extension-warpy
ImgLib2 RealTransform brought to QuPathqupath-groovy-python-runner
A proof of concept to run python segmentations and recovering the results within QuPathijp-LaRoMe
some useful function to get Label from ROIs and vice versa , and more!ijp-kheops
EasyXT-FIJI
Commands and Classes for interfacing between Imaris and Fijiijp-operetta-importer
PerkinElmer Operetta Importer using BioFormats!ijp-max-inscribed-circles
ImageJ/Fiji plugin that fills a mask or selection with the largest inscribed cirlcesbigdataviewer-omero
Repository to open OMERO multiresolution images in BigDataViewerqupath-scripts
This repository contains Scripts we found useful when using QuPathqupath-extension-abba
QuPath extension for Aligning Big Brains and Atlasesbiop-bash-scripts
Bash scripts to simplify your life (let's hope so!)bigdataviewer-biop-tools
Another repo for bdv tools.ijp-DEVILS
DEVILS (Display Enhancement for Visual Inspection in Large Stack) is an ImageJ plugin.ijp-frc
Making use of the Fourier Ring Correlation Implementation by Alex Herbert which is itself 'adapted from the FIRE (Fourier Image REsolution) plugin produced as part of the paper Niewenhuizen, et al (2013). Measuring image resolution in optical nanoscopy. Nature Methods, 10, 557 http://www.nature.com/nmeth/journal/v10/n6/full/nmeth.2448.htmlnapari-figure
a napari plugin to make figurecoLoc
A Board Game to teach co-localization analysisqupath-biop-extensions
Extensions for QuPath, written by the BIOPbigdataviewer-image-loaders
quick-start-czi-reader
A bio-formats image reader for CZI that starts fasterbigdataviewer-bioformats
Opens bio-formats images in BigDataViewergist-query
Query Gists by the BIOP and add them into a table format compatible with C4Sciencebigdataviewer_scijava
OBSOLETE replaced by bigdataviewer playground - Scijava commands for starting BigDataViewer and exporting data.EasyXT
EasyXT is an extension for Imarisabba_python
ABBA, controlled from pythonijab-biop-channel-tools
Tools to ease propagation of channel settings (B&C, LUT) to many images Includes super montage options See https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/imagej_tools/ijab-biop_channel_tools/tool-ibidi-slide-holder
3D model and instructions for adapting the Operetta CLS slide holder to work with IBIDI removable chamber slidesOMERO-scripts
Series of script to make use of OMERObigdataviewer-playground-display
Display additions for bigdataviewer using bigdataviewer-playgroundqupath-general-scripts
General Scripts for QuPathArgoLight_analysis_tool
Code to control the quality of images taken with our microscopesbiop-desktop-doc
The documentation of the BIOP-desktopBIOP-desktop
ijp-siftalignmultichannel-ij2
Extension of the SIFT align Fiji plugin which handles multichannel imagesijp-gabriel-graph
HuygensScripts
Python scripts to use within HuygensPro consoleIPA4LS
Code and Examples, Image Processing & Analysis for Life Scientists, Part Two. This course is only given at EPFL.qupath-extension-biop
An extension for QuPath with some tools made at the BIOP.EasyXT-GUI
A simple Matlab GUI to leverage EasyXT and centralize complex analysis pipelines in Imarisbiop-operetta-tools
Scripts and tools to use for the PerkinElmer Operetta Systemijs-TrackMate
some groovy scripts to use TrackMateijab-sim-storm-tools
ActionBar containing the tools for Correlative SIM STORMbigdataviewer-selector
Source Selection mode for BigDataViewerijp-jacop-b
Jacop by F. Cordeliรจres revamped by the BIOPabba-installer
Repository backing the creation of standalone installers for ABBAlightsheet-brain-workflows
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