Segmentation of bacteria growing in agar-pads, imaged by de-focused transmitted light stacks
- 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 |
|---|---|---|
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Samples provided by Daniel Thédié, El Karoui Lab, University of Edinburg
- 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
Check the wiki!