Closed ambrosejcarr closed 4 years ago
This would be really useful for us. I think it would be nice if the code to convert a probability image to a cell label image wasSegmentationMaskCollection
constructor we can input probability images from other segmentation pipelines.
Cell Profiler's Ilastik tie-in is as follows: https://github.com/CellProfiler/CellProfiler/wiki/How-to-use-Pixel-Classification-in-CellProfiler
I interpret this as shelling out, not calling Ilastik directly from their python code, which may induce portability problems.
Objective
As a user relying on a 3rd party automated segmentation tools, I want to assign spots to cells using a pre-trained model so that I can generate a spatially annotated gene expression matrix.
I want starfish to orchestrate this so that I can take advantage of starfish’s image processing before segmentation and track the provenance of my segmentation results.
Acceptance Criteria
Notes & reference material
From @ambrosejcarr:
starfish.image.Segment.IlasticPretrained(imagestack, path_to_ilastic_model, threshold, cell_label=0)
.skimage.feature.label
to extract the nucleiSegmentationMaskCollection.from_label_image
Validation