Machine learning

BioImage.IO -- a collaborative effort to bring AI models to the bioimaging community. 

• Integrated with Fiji, ilastik, ImJoy and more
• Try model instantly with BioEngine
• Contribute your models via Github

This is a database of pretrained deep Learning models. 

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 

LOBSTER (Little Objects Segmentation and Tracking Environment), an environment designed to help scientists design and customize image analysis workflows to accurately characterize biological objects from a broad range of fluorescence microscopy images, including large images, i.e. terabytes of data, exceeding workstation main memory.

• 75 workflows available 
• no programming, with GUI
• matlab based 

Web based application for deep learning cell classifier . Aim to replace cellprofiler analyst and advanced cell classifier.

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.