Automated

ImageM integrates into a GUI several algorithms for interactive image processing and analysis. Interface is largely inspired from the open source software "ImageJ".

Yet another pixel classifier Yapic is a deep learning tool to :

train your own filter to enhance the structure of your choice 

train multiple filter at once 

it is based on the u-net convolutional filter . 

To train it : annotation can come from example from Ilastik software , tif labelled files can be transferred to yapic. 

Training takes about hours to days , prediction takes seconds once trained .

It can be ran from command line .

note that only 10 to 20 images with sparse labeling are required for efficient training 

This is the ImageJ/Fiji plugin for StarDist, a cell/nuclei detection method for microscopy images with star-convex shape priors ( typically for Dapi like staining of nuclei). The plugin can be used to apply already trained models to new images.

The Morphonet Python API provide an easy interface to interact directly with the MorphoNet server. Very useful to upload, download your dataset and superimpose on it any quantitative and quantitative informations.

Vaa3d BJUT Fast Marching Spanning Tree algorithm dockerised workflow for BIAFLOWS