bioimage-informatics

QuPath - Bioimage analysis & digital pathology

Data-efficient and weakly supervised computational pathology on whole slide images - Nature Biomedical Engineering

A Python toolkit for pathology image analysis algorithms.

AI-based pathology predicts origins for cancers of unknown primary - Nature

The official deployment of the Digital Slide Archive and HistomicsTK.

C++ library and command-line software for processing and analysis of terabyte-scale volume images locally or on a computing cluster.

SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.

Fast and Scalable Image Search for Histology

A Fiji plugin that automatically quantify synapses from multi-channel fluorescence microscopy images.

CellOrganizer for Docker

ViCAR extracts and employs (Vi)sual (C)ues for an (A)daptive (R)egistration of time-lapse image data recorded in microfluidic devices.

SeeVIS is a (S)egmentation-fr(ee) (VIS)ualization pipeline for time-lapse image data. It comprises three steps: 1. preprocessing, 2. feature extraction, and 3. an extended version of the space time cube with three novel color mappings adapted to cell colony growth.

CYCASP is a methodology for investigating and understanding (C)olon(Y) growth and (C)ell (A)ttributes at the population level. It couples (SP)atiotemporal changes by relying on two novel data abstractions and a modular algorithm.

CellOrganizer on Jupyter Notebook

Analysis of single molecule localization microscopy. 'pointpattern': statistical analysis. 'image': image processing+analysis+classification