Dask chunk-wise cell labeling in large-scale images

At the Jackson Laboratory we’ve been working on a dask-based labeling tool to address chunk-wise labeling of largescale images with objects that “touch”.
In contrast with the label module in dask-image, this should handle the output of deep-learning segmentation methods, such as cellpose, stardist, hover-net, etc. on touching cell images that cannot be addressed by simply merging connected components like in the current label method.

The use case is to segment large-scale images (e.g. Whole slide images) in an efficient manner.
The tool can be found in this repo https://github.com/TheJacksonLaboratory/dask_relabeling.git and there are a pair of examples of the tool.

I would appreciate any feedback and also know if people are interested in doing this kind of large-scale analysis.

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Hi @fercer, welcome to Dask Discourse forum, and thanks for sharing this!

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