[FLIMfit-users] Segmentation problems on FLIMfit on macOS Sierra

[R.F. Laine]

Hi Ian,
Thanks for your quick reply.
I actually went back to the data to understand the problem better and 
realised it is also a problem on the PC version (therefore not OS 
related). This seems to be to do with the fact that only the image on 
which a segmentation has been performed have a non-zero segmentation 
image when OK-ing the Segmentation manager window. I think the problem 
then stems down to the default behaviour of a non-segmented image (all 0 
or all 1). It is currently set to define an empty segmentation image for 
non-segmented image.

This can be circumvented by selecting the whole image as the 
segmentation image for these. But it would make more sense to me if it 
was the opposite (non-segmented image are fully kept), as this would be 
more easily compatible with the intensity threshold.

Sorry for posting a problem without fully exploring it before.
This should be taken as a suggestion of improvement rather than bug 
report then !

Cheers,

Romain


On 2017-03-22 15:50, Munro, Ian via FLIMfit-users wrote:
> Thanks for reporting that Romain.
> I’ll have a look and get back to you as soon as I can.
> 
> Ian
> 
> 
>> On 22 Mar 2017, at 11:45, R.F. Laine via FLIMfit-users 
>> <flimfit-users at lists.openmicroscopy.org.uk> wrote:
>> 
>> Dear all,
>> One of our collaborators is using FLIMfit to analyse some of our FLIM 
>> data. However, there seems to be an issue with the segmentation 
>> manager on the mac version that I do not have on my PC.
>> 
>> Please see below the description of the issue:
>> 
>> Machine: macOS Sierra 10.12.3, FLIMfit 4.12.1
>> Description: When using the segmentation manager when multiple images 
>> are loaded, if one image is manually segmented, the other images 
>> subsequently appear black and can therefore not be analysed. This can 
>> only be resolved when the manual segmentation is deleted. As such, it 
>> is not possible to analyse multiple images when one image of the 
>> series has to be manually segmented. This happens with every dataset 
>> that I load.
>> 
>> Has anyone observed/solved this?
>> 
>> Many thanks !
>> 
>> Romain
>> 
>> --
>> Dr. Romain Laine, PhD in Biophotonics
>> Laser Analytics Group
>> Department of Chemical Engineering and Biotechnology
>> University of Cambridge
>> West Cambridge Site
>> Philippa Fawcett Drive
>> Cambridge
>> CB3 0AS
>> _______________________________________________
>> FLIMfit-users mailing list
>> FLIMfit-users at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/flimfit-users
> 
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-- 
Dr. Romain Laine, PhD in Biophotonics
Laser Analytics Group
Department of Chemical Engineering and Biotechnology
University of Cambridge
West Cambridge Site
Philippa Fawcett Drive
Cambridge
CB3 0AS