Re-occurs among tags (visualisation, rendering, viewer, classification, ...)|ToDo: Clear up relation between Classification, Clustering, and Prediction and recognition (also in main EDAM)



ImJoy is a plugin powered hybrid computing platform for deploying deep learning applications such as advanced image analysis tools. ImJoy runs on mobile and desktop environment cross different operating systems, plugins can run in the browser, localhost, remote and cloud servers.With ImJoy, delivering Deep Learning tools to the end users is simple and easy thanks to its flexible plugin system and shareable plugin URL. Developers can easily add rich and interactive web interfaces to existing Python code.




CRImage a package to classify cells and calculate tumour cellularity

CRImage provides functionality to process and analyze images, in particular to classify cells in biological images. Furthermore, in the context of tumor images, it provides functionality to calculate tumour cellularity.

has function



Multicut workflow for large connectomics data. Using luigi for pipelining and caching processing steps. Most of the computations are done out-of-core using hdf5 as backend and implementations from nifty

Spine classification based on kernel density estimation


We propose to use a kernel density estimation (KDE) based approach for classification. This non-parametric approach intrinsically provides the likelihood of membership for each class in a principled manner. The implementation was used in Ghani2016. Any papers using this code should cite Ghani2016 accordingly. The software has been tested under Matlab R2013b.


Sample Data: Annotated two-photon images of dendritic spines