jamesMo84

Deepcell segmentation without cytoplasm channel

1

I note that Deepcell provides both a segmentation (nuclear channel only) and mesmer (nuclear and cytoplasm) model (https://www.deepcell.org/predict) Our datasets do not have a single general cytoplasm marker that will...

Squidpy comparative statistics

1

We’re looking to use squidpy to generate comparative spatial statistics across multiple samples. I see we can supply the sample key by ```library_key``` in ```squidpy.gr.spatial_neighbors``` so that the spatial graph...

supplying additional groupings

2

Just wondering if there is support to add additional arguments into some functions to change the way the data is grouped other than by 'imageid'. eg in tl.foldchange 'from_group' could...

Local Deepcell or Cellpose server for larger tile segmentation

2

Hi, Great package, I've started applying the pipeline to TMA cores but am running into the issue with Deepcell Kiosk max tile size of 2048x2048. Is there scope to specify...