2d auto segmentation

[Nal44]

Hi,

I am testing 2d .

the auto segmentation runs, but doesn't give any outputs (with default parameters) ... ?

Any ideas ?

thanks
antho

[Nal44]

I can share an image if that helps ?

[constantinpape]

If you're using the vit_b_lm then you need to set lower values for the thresholds:

pred_iou_thresh = 0.65, stability_score_thresh = 0.75

We are working on setting these thresholds automatically, see #337.

[Nal44]

Thanks a lot,
using vit_b_lm and pred_iou_thresh = 0.65, stability_score_thresh = 0.75 as suggested :

see below :
I think it needs it might need pre filtering or some normalization step ?

Any ideas ?
thanks

[constantinpape]

Yes, I think the cells are too small for the current settings of the automated segmentation. I think it is more promising if you follow the approach outlined in #383. For this the automatic segmentation results don't really matter. As long as manual annotation either via point or bounding box prompts works well the refinement approach should work.

[Nal44]

ok, no probs,
working on it :)

(For info ,this is a standard 20x objective image that we use for staining in the lab)