BIOP/qupath-groovy-python-runner

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Created almost 4 years ago
Updated almost 4 years ago

BIOP/qupath-groovy-python-runner

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

qupath-extension-cellpose

an extension that wraps a Cellpose environment such that WSI can be analyzed using Cellpose through QuPath.

Jupyter Notebook

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)

IPA4LSx

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

qupath-extension-warpy

ImgLib2 RealTransform brought to QuPath

ijp-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 Fiji

ijp-operetta-importer

PerkinElmer Operetta Importer using BioFormats!

ijp-max-inscribed-circles

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

bigdataviewer-omero

Repository to open OMERO multiresolution images in BigDataViewer

qupath-scripts

This repository contains Scripts we found useful when using QuPath

qupath-extension-abba

QuPath extension for Aligning Big Brains and Atlases

biop-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.html

napari-figure

a napari plugin to make figure

coLoc

A Board Game to teach co-localization analysis

qupath-biop-extensions

Extensions for QuPath, written by the BIOP

bigdataviewer-image-loaders

quick-start-czi-reader

A bio-formats image reader for CZI that starts faster

bigdataviewer-bioformats

Opens bio-formats images in BigDataViewer

gist-query

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

Jupyter Notebook

bigdataviewer_scijava

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

EasyXT

EasyXT is an extension for Imaris

abba_python

ABBA, controlled from python

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/

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

bigdataviewer-playground-display

Display additions for bigdataviewer using bigdataviewer-playground

qupath-general-scripts

General Scripts for QuPath

ArgoLight_analysis_tool

Code to control the quality of images taken with our microscopes

biop-desktop-doc

The documentation of the BIOP-desktop

BIOP-desktop

ijp-siftalignmultichannel-ij2

Extension of the SIFT align Fiji plugin which handles multichannel images

ijp-gabriel-graph

HuygensScripts

Python scripts to use within HuygensPro console

IPA4LS

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 Imaris

biop-operetta-tools

Scripts and tools to use for the PerkinElmer Operetta System

ijs-TrackMate

some groovy scripts to use TrackMate

ijp-multi-stack-montage

An ImageJ1 plugin for making montages out of stacks

ijab-sim-storm-tools

ActionBar containing the tools for Correlative SIM STORM

bigdataviewer-selector

Source Selection mode for BigDataViewer

ijp-jacop-b

Jacop by F. Cordelières revamped by the BIOP

abba-installer

Repository backing the creation of standalone installers for ABBA

lightsheet-brain-workflows