Failed Segmentation

[fish-quant]

Failed Segmentation

[Henley13]

Hi @IrisWEI-1996,

Yes I have already seen this bug. Your masks are ok, but the boundary line extracted from them seems so thin, that matplotlib fails to show them correctly. Two solutions:

• You could use a bigger framesize.
• I should add a parameter in the plot function to allow the user enlarging the boundaries... Sometimes you want a small plot (a small framesize), but in these cases, pixel-large boundaries might fail to appear.

Could you tell me if the framesize trick is working ? Otherwise, could you give me your big-fish version and the versions of your dependencies ?

[IrisWEI-1996]

Hi Henley,

Thank you for your rapid reply and the suggestion!
Yes, the framesize works and now I can see the boundary! Another question is that I suppose the nucleus should be seen in the picture but not here, do you have any suggestions on that?

Thanks again,
Iris

[Henley13]

Hi @IrisWEI-1996,

Good for your plot! I should definitely add a parameter to tune the boundary width if the user want to. Concerning your nuclei, I do not know. Do they appear in the image you provided in the image parameter ? The fluorescent label you used in this image seems to stay outside the nuclei.

Arthur

[IrisWEI-1996]

Hi @Henley13 ,

That sounds great and helpful! Many thanks for the suggestions again!
Regarding the nuclei problem, yes you are right, the original picture is with cytoplasm only. I misunderstood that it would plot an integration of two parts but now it's clear to me, and I will close this issue.

All the best,
Iris