Discover BIOP/qupath-extension-cellpose Open Source project

Wrappers for external software calls (Cellpose, Elastix, Ilastix...) and java utilities (object conversions and display)

ijl-utilities-wrappers

ImageJ Macro Scripts showcased during Image Processing and Analysis for Life Scientists MOOC on EdX

IPA4LSx

qupath-extension-warpy

ImgLib2 RealTransform brought to QuPath

A proof of concept to run python segmentations and recovering the results within QuPath

qupath-groovy-python-runner

some useful function to get Label from ROIs and vice versa , and more!

ijp-LaRoMe

ijp-kheops

Commands and Classes for interfacing between Imaris and Fiji

EasyXT-FIJI

PerkinElmer Operetta Importer using BioFormats!

ijp-operetta-importer

HTML

ijp-max-inscribed-circles

ImageJ/Fiji plugin that fills a mask or selection with the largest inscribed cirlces

Repository to open OMERO multiresolution images in BigDataViewer

bigdataviewer-omero

This repository contains Scripts we found useful when using QuPath

qupath-scripts

QuPath extension for Aligning Big Brains and Atlases

qupath-extension-abba

Bash scripts to simplify your life (let's hope so!)

biop-bash-scripts

Shell

bigdataviewer-biop-tools

Another repo for bdv tools.

DEVILS (Display Enhancement for Visual Inspection in Large Stack) is an ImageJ plugin.

ijp-DEVILS

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.html

ijp-frc

a napari plugin to make figure

napari-figure

A Board Game to teach co-localization analysis

coLoc

qupath-biop-extensions

Extensions for QuPath, written by the BIOP

bigdataviewer-image-loaders

A bio-formats image reader for CZI that starts faster

quick-start-czi-reader

Opens bio-formats images in BigDataViewer

bigdataviewer-bioformats

Query Gists by the BIOP and add them into a table format compatible with C4Science

gist-query

Jupyter Notebook

bigdataviewer_scijava

OBSOLETE replaced by bigdataviewer playground - Scijava commands for starting BigDataViewer and exporting data.

EasyXT is an extension for Imaris

EasyXT

MATLAB

abba_python

ABBA, controlled from python

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/

ijab-biop-channel-tools

Batchfile

tool-ibidi-slide-holder

3D model and instructions for adapting the Operetta CLS slide holder to work with IBIDI removable chamber slides

OMERO-scripts

Series of script to make use of OMERO

Display additions for bigdataviewer using bigdataviewer-playground

bigdataviewer-playground-display

General Scripts for QuPath

qupath-general-scripts

ArgoLight_analysis_tool

Code to control the quality of images taken with our microscopes

The documentation of the BIOP-desktop

biop-desktop-doc

BIOP-desktop

JavaScript

ijp-siftalignmultichannel-ij2

Extension of the SIFT align Fiji plugin which handles multichannel images

ijp-gabriel-graph

Python scripts to use within HuygensPro console

HuygensScripts

Code and Examples, Image Processing & Analysis for Life Scientists, Part Two. This course is only given at EPFL.

IPA4LS

qupath-extension-biop

An extension for QuPath with some tools made at the BIOP.

A simple Matlab GUI to leverage EasyXT and centralize complex analysis pipelines in Imaris

EasyXT-GUI

MATLAB

biop-operetta-tools

Scripts and tools to use for the PerkinElmer Operetta System

some groovy scripts to use TrackMate

ijs-TrackMate

An ImageJ1 plugin for making montages out of stacks

ijp-multi-stack-montage

ActionBar containing the tools for Correlative SIM STORM

ijab-sim-storm-tools

bigdataviewer-selector

Source Selection mode for BigDataViewer

Jacop by F. Cordelières revamped by the BIOP

ijp-jacop-b

Repository backing the creation of standalone installers for ABBA

abba-installer

lightsheet-brain-workflows