Component

A Component is an implementation of certain image processing / analysis algorithms.

Each component alone does not solve a Bioimage Analysis problem.

These problems can be addressed by combining such components into workflows.

Description

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 

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Description

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

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Description

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.

Stardist
Description

 

Deep learning based web app upload your data and get segmentation

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cellpose