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2022-image-processing-overview

A brief glossary of image processing terms for pathologists

2022-qupath-cell-detection

Images & code to visualize to illustrate the challenges image analysis in pathology

analysis-parameter-demo

aria

Retinal vessel analysis software for MATLAB

bioformats

Bio-Formats is a Java library for reading and writing data in life sciences image file formats. It is developed by the Open Microscopy Environment. Bio-Formats is released under the GNU General Public License (GPL); commercial licenses are available from Glencoe Software.

bioimagebook.github.io

An introduction to bioimage analysis - http://bioimagebook.github.io

cell_detection_approaches

Bioimage analysis pipelines to detect cells (nucleus + cytoplasm) and generate label images with the aim of establishing an object hierarchy

colormap

A Java package for generating and using linear and categorical colormaps.

core-bioimage-io-python

Python specific core utilities for interpretation of specification files of the bioimage model zoo

cpu-sampler-extension

djl

An Engine-Agnostic Deep Learning Framework in Java

djl-tensorflow-javacpp

Testing the use of Deep Java Library with TensorFlow & other JavaCPP dependencies

fluorescence-simulator

A simple ImageJ plugin to simulate blur and noise from fluorescence imaging

gradle-javacpp

Gradle plugins to automate the build process of JavaCPP and JavaCV

homebrew-qupath

Experimental homebrew tap for QuPath-related dependencies

icc-profiles

Checking how to apply ICC Profiles in Python and Java

image-analysis-scripts

Various scripts written for image analysis utilities

imagej-intro

OUT-OF-DATE! The new book is at https://bioimagebook.github.io

imagej-plugins

ImageJ plugins written to help develop https://bioimagebook.github.io

imagej1

Wayne Rasband's ImageJ 1.x repository, updated once a night. To develop this code, use https://github.com/imagej/ImageJA.

imagejts-tools

Example ImageJ plugins to convert ROIs to and from GeoJSON

imglib2-exploring

java-bioimage-io

Java specific core utilities for interpretation of specification files of the bioimage model zoo

javafx-ui-template

Project providing a simple template for creating a JavaFX UI component for use with QuPath

jpen

Java library for accessing pen/digitizer tablets and pointing devices

log-viewer

meta

A community dedicated to supporting tools for technical and scientific communication and interactive computing

models

Trained models for use with QuPath

ome-codecs

OME image compression (coder-decoder implementations)

openmicroanatomy-qupath-extension