Data and similar resources.
Trained networks
We made the following already trained networks designed to specific tasks freely available together with example and training data.
Cytosol and nucleus 2D segmentation
StarDist 2D segmentation of nucleus (DAPI) and U-net segmentation of cytoplasm (phalloidin staining).
Download training data and networks:
- images.zip
- masks.zip
- cyto
- nucleus
Format of input file is a 16-bit raw TIFF with 3 channels (i..e. POI, phalloidin, DAPI).
Run the prediction by:
conda create -n cytnuc
python
By default the first channel is channel of interest (e.g. staining), the second channel is phalloidin and the third channel is DAPI.
The output is a CSV file with the following structure:
Text
Microtubuli individual segmentation 3D
Microtubuli labeled by GFP in U2-OS cells.
Paramecium cilia 3D segmentation
Cilia of P.tetraulia with monoclonal antibody targeting tubulin (clone: AXO49).
40x epifluorescence z-stacks as input (non-confocal).
