Metadata-Version: 2.1
Name: TaLiSSman
Version: 0.0.3
Summary: Segmentation of bacteria growing in agar-pads, imaged by transmitted light stacks
Home-page: https://github.com/jeanollion/talissman
Author: Jean Ollion
Author-email: jean.ollion@polytechnique.org
License: UNKNOWN
Download-URL: https://github.com/jeanollion/TaLiSSman/archive/0.0.3.tar.gz
Description: # TaLiSSman: TrAnsmitted LIght Stack SegMentAtioN
        Segmentation of bacteria growing in agar-pads, imaged by de-focused transmitted light stacks
        
        ## How it works
        - Expected input images are stacks of 2D images, with Z-axis last : Image = [batch, Y, X, Z]. We advise stacks of 5 slices with a 0.2µm step, in range [-0.6µm, -1.4µm] (relatively to the focal plane)
        - Segmentation is performed by regression of the Euclidean Distance Map (EDM).
        - This repository does not include the downstream watershed step to obtain labeled images.
        
        | Input Transmitted-Light Stack | Predicted EDM | Segmented Bacteria |
        | :---:         |          :---: |          :---: |
        | <img src="../../wiki/resources/inputStackREV.gif" width="300"> | <img src="../../wiki/resources/edm.png" width="300">    | <img src="../../wiki/resources/outputStackREV.gif" width="300"> |
        
        Samples provided by Daniel Thédié, <a href="http://www.elkarouilab.fr/">El Karoui Lab</a>, University of Edinburg
        
        ## Network architecture:
        - Based on U-net
        - Before first layer a block is added to reduced Z-axis using 3D convolutions and 3D Z-maxpooling
        
        More details can be found on my [website](https://www.sabilab.fr/project/2021/12/21/talissman.html)
        
        ## How to use it
        Check the [wiki](../../wiki)! 
        
Keywords: Segmentation,Bacteria,Transmitted Light,Bright Field,Stack,Microscopy
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
Classifier: Topic :: Scientific/Engineering :: Image Processing
Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
Classifier: Programming Language :: Python :: 3
Requires-Python: >=3
Description-Content-Type: text/markdown
