BioImaging And Optics Platform (BIOP)

IPA4LSx

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

qupath-groovy-python-runner

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

qupath-biop-extensions

Extensions for QuPath, written by the BIOP

bigdataviewer_scijava

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

EasyXT

EasyXT is an extension for Imaris

gist-query

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

ijab-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/

EasyXT-GUI

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

HuygensScripts

Python scripts to use within HuygensPro console

ijab-sim-storm-tools

ActionBar containing the tools for Correlative SIM STORM

ijs-TrackMate

some groovy scripts to use TrackMate

IPA4LS

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

QuMark

A standardized benchmark for evaluating QuPath performance

bigdataviewer-uberdataset

This repository contains functions to combine several xml bigdataviewer datasets into a single one, called a uberdataset.

BIOP-Dataset

BIOP-Educational-Figures

clij2-fft

IJ-Plugin_JACoP

Just Another Colocalisation Plugin

ijab-biop-basics

Template macro compatible with BIOP Basics

ijab-biop-common-tools

Common Tools and Shortcuts for simplifying everyday work with biological images

ijab-ihc-ratio

ijab-IHC-Ratio

ijab-mutli-manual-select

ijab-tracmit

TRACMIT: an effective pipeline for tracking and analyzing cells on micropatterns through mitosis

ijp-biop-run-macro

Macro Runner with SciJava Parameters

ijp-lima-biop

CellProfiler/FIJI ImageJ Bridge + LiMA Helper class

ijp-localizej

ImageJ plugin for the Simulation of localization-based nanoscopy

ijp-quality-filter

Short plugin that takes the ratio of the mean intensity of an ROI wrt the mean intensity of a surrounding band to assess the quality of the detection.

OrientationJ

ImageJ's plugin for directional analysis in images: color-coded analysis, distribution of orientation, vector field, keypoint detection

qupath-biop-extensions-docs

Javadoc for our BIOP Extensions

stardist-imagej