[BUG] min_size argument unused

[SimonBon]

Hello everyone,

I use Cellpose to segment images of DAPI stained single cells and, sometimes we have some artefacts in the images which made me want to use the min_size argument of the .eval function of CellposeModel. After trying out some values and plotting the results I realised that changing the value did not filter out the small segmentation masks.

What I do is I have a grayscale image that I pass to the eval function using the following line:

masks, _, _ = model.eval(img[...,2], diameter=60, min_size=2000)

If I go into the function that I assume to be responsible to remove small segmentations I see the following after using the following print statement (print(npix, min_size)):

...
1983 15
2371 15
3218 15
2663 15
1762 15
3247 15
1649 15
...

I the working solution for me right know is to pass the min_size argument for function dynamics.compute_masks on line 652 in module cellpose.models

without fix:

with fix:

Thanks for your help!

[ashishUthama]

Also see #280

[mrariden]

@SimonBon thanks for identifying and testing a solution. Do you want to make a PR with the changes so you'll get credit in the release notes?

[SimonBon]

@mrariden done so, see #773. Thanks