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

[Sean Warren]

Hi Romain,

Thanks for the feedback. This is something I've discussed with others before.
I am happy to change the default behaviour here, unless any other users are relying on this?

Thanks
Sean
________________________________

Dr. Sean Warren | Research Officer
Invasion and Metastasis
Cancer Division
Garvan Institute of Medical Research
The Kinghorn Cancer Centre, 370 Victoria Street, Darlinghurst, NSW 2010

T: + 61 (0)2 9355 5852 I E: s.warren at garvan.org.au

http://www.garvan.org.au/research/cancer/invasion-and-metastasis

________________________________________
From: FLIMfit-users [flimfit-users-bounces at lists.openmicroscopy.org.uk] on behalf of R.F. Laine via FLIMfit-users [flimfit-users at lists.openmicroscopy.org.uk]
Sent: Thursday, 23 March 2017 03:09
To: Munro, Ian
Cc: flimfit-users at lists.openmicroscopy.org.uk
Subject: Re: [FLIMfit-users] Segmentation problems on FLIMfit on macOS Sierra

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
>
> _______________________________________________
> FLIMfit-users mailing list
> FLIMfit-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/flimfit-users

--
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
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