cellpose
is a set of segmentation network models for anatomical segmentation of cells in microscopy images. We have written the Mantle cellpose-segmentation
pipeline to read image directories from your Mantle Database, perform segmentation using cellpose
, and write the resulting masks to your Mantle Database.
image_directory
data type. Expand to view the properties of image_directory
entities:
Properties
Ljosa, V., Sokolnicki, K. L., & Carpenter, A. E. (2012). Annotated high-throughput microscopy image sets for validation. Nature Methods, 9(7), 637-637.These images are taken from human MCF7 (human breast adenocarcinoma) and A549 (human alveolar basal epithelial) cell lines that are stained for 1) DNA and 2) NFκB. The cells are plated on a 96-well plate and each well was treated with one of 12 concentration points of TNFα. Higher concentrations of TNFα should induce cytoplasm to nucleus translocation of NFκB. 2-channel images were acquired from this experiment (channel 1: DNA, channel 2: NFκB).
cellpose-segmentation
pipeline adapts the Cellpose CLI to allow it to take image_directory
entities as inputs and to structure the output directory of masks into a segmentation_mask_directory
entity.
Expand to view the parameters for the cellpose-segmentation
pipeline:
Input parameters
None
can be used for automatic estimation of the object diameter by Cellpose.