CellPose

Node using cellpose's deeplearning-based cellular segmentation to automatically predict cellular instances without need for manual thresholds. Requires pypi package cellpose>=0.6.0 to be present in the set conda environment.

Will only predict on 2D, 3D, 2D+T images and does not perform NMS / instance linking.

Stringer, C., Wang, T., Michaelos, M. et al. Cellpose: a generalist algorithm for cellular segmentation. Nat Methods 18, 100–106 (2021). https://doi.org/10.1038/s41592-020-01018-x

Input ports

1. Type: Table
   Input
   Input table containing an image column on which cellpose will predict.

Output ports

1. Type: Table
   Output
   Table containing an additional column named "INPUT-NAME_PREDICTION-SUFFIX" containing a segmentation map of predicted cells.