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).

Input data for cell segmentation and reference masks and edge weights used for training.

Bacteria fluorescent segmentation from DAPI 

E.coli and S.enterica segmentation from 16-bit monochrome DAPI images. Uses StarDist2D.

Original Image Output segmented cells
Modified Image Input 16-bit DAPI image

Training data and reference ground truth masks created by Storm Phillipson.


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).

Segmentation masks created by Trupthi Josh
Paramecium 2D segmentation and tracking
Low-resolution 3D segmentation of single-molecules
High-resolution 3D segmentation of single-molecules