BioImaging And Optics Platform (BIOP)'s repositories
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 QuPath
ijl-utilities-wrappers
Wrappers for external software calls (Cellpose, Elastix, Ilastix...) and java utilities (object conversions and display)
EasyXT-FIJI
Commands and Classes for interfacing between Imaris and Fiji
ijp-operetta-importer
PerkinElmer Operetta Importer using BioFormats!
biop-bash-scripts
Bash scripts to simplify your life (let's hope so!)
abba_python
ABBA, controlled from python
qupath-extension-abba
QuPath extension for Aligning Big Brains and Atlases
qupath-scripts
This repository contains Scripts we found useful when using QuPath
bigdataviewer-biop-tools
Another repo for bdv tools.
quick-start-czi-reader
A bio-formats image reader for CZI that starts faster
qupath-extension-biop-omero
QuPath extension to work with images through OMERO's Java API (raw)
ArgoLight_analysis_tool
Code to control the quality of images taken with our microscopes
bigdataviewer-playground-display
Display additions for bigdataviewer using bigdataviewer-playground
OMERO-scripts
Series of script to make use of OMERO
abba-documentation
Documentation for ABBA - Aligning Big Brains & Atlases
bigdataviewer-selector
Source Selection mode for BigDataViewer
ijp-jacop-b
Jacop by F. Cordelières revamped by the BIOP
ijp-template-ij2
Template for ImageJ2 command for the PT-BIOP.
cellpose
a generalist algorithm for cellular segmentation with human-in-the-loop capabilities
pcb-02-fiji
Repo with example scripts from out Practical Course BIOP: Fiji for Everyday Tasks
qupath
QuPath - Bioimage analysis & digital pathology
super-nice-pypi-package
blabla