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flimfit / FLIMfit

State of the art fluorescence lifetime imaging analysis software
http://flimfit.org
GNU General Public License v2.0
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FLIMfitFrontEnd #350

Closed AndreZeug closed 5 years ago

AndreZeug commented 5 years ago

updating bfopen, OMERO, etc. cauese error in websave.m (line 159) if library_path folder 'ThirdParty' does not exist, which supposed to be a subfolder of FLIMfitFrontEnd?

It also requires to start FLIMfit inside FLIMfitFrontEnd folder direct path to folder 'ThirdParty' would be more convenient, this would allow FLIMfit from any working directory if FLIMfitFrontEnd is part of Matlab path

seanwarren commented 5 years ago

Thanks for picking this up; this should be resolved now

AndreZeug commented 5 years ago

Thanks for fixing: Briefly checked. just running FLIMfit out of Matlab Command (and deleting folder ThirdParty before) still causes following error when pwd is not FLIMfitFrontEnd:

FLIMfit Downloading bioformats... Error using movefile No matching files were found.

Error in get_bioformats (line 21) movefile('ThirdParty\bfmatlab\bioformats_package.jar','ThirdParty\bfmatlab\bioformats_package.zip')

Error in addpath_global_analysis (line 56) get_bioformats(thirdpartydir,'5.8.2');

Error in FLIMfit (line 29) addpath_global_analysis();

21 movefile('ThirdParty\bfmatlab\bioformats_package.jar','ThirdParty\bfmatlab\bioformats_package.zip') K>>

could you please add 'thisdir' to the 'movefile' commands?

Thanks (hope I did not do something wrong)

seanwarren commented 5 years ago

Thanks Andre - this should be properly fixed now!

AndreZeug commented 5 years ago

Dear Sean, short but important question: is there a chance to import 'ptu' data taken with bi-directional scan (@ Leica SP8 FALCON)?

We already acquired substantial amount of data in bi-directional scan mode, but realized now that standard import into FLIMfit result in 'mirror images' (due to line averaging). Question is if we should switch back to uni-directional scan mode to allow analysis in in FLIMfit.

Best

Andre

Von: Sean Warren notifications@github.com Gesendet: Mittwoch, 15. August 2018 09:06 An: flimfit/FLIMfit FLIMfit@noreply.github.com Cc: Zeug, Andre Dr. Zeug.Andre@mh-hannover.de; Author author@noreply.github.com Betreff: Re: [flimfit/FLIMfit] FLIMfitFrontEnd (#350)

Thanks Andre - this should be properly fixed now!

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seanwarren commented 5 years ago

Hi Andre,

FLIMfit does support bi-directional scan in principle although it obviously isn't recognizing the header information correctly from your PTU file - please could you send me a file with a bidirectional scan and I'll have a look? I think we should be able to resolve this quite easily.

Thanks Sean

imunro commented 5 years ago

Bio-formats seems to support some Leica formats but I can't see .ptu on the list: https://docs.openmicroscopy.org/bio-formats/5.9.2/supported-formats.html

AndreZeug commented 5 years ago

Dear Sean, thank you very much for your immediate response. Would be great if we can analyse our data with FLIMfit. You can find some data here: https://www.mh-hannover.de/cellneurophys/zeug/FLIMfit/

Thank you so much,

Andre

AndreZeug commented 5 years ago

Dear Sean, sorry, but may be my problem originates from the fact, that I use your compiled version of FLIMReader (from August 3rd) because I am not able to compile by myself. So I might not have the latest version of it. Probably I 'only' need to learn how to compile FLIMReader by myself.

@imunro: 'ptu' is originally PicoQuant data type, which Leica uses as well, since they implemented PicoQuant technique to their system.

seanwarren commented 5 years ago

Hi Andre,

There haven't been any significant changes since then so I don't think that will be the problem. I'll try and have a look at your data tomorrow

Cheers Sean

seanwarren commented 5 years ago

Hi Andre,

I've had a look at the file, Leica organise their bidirectional data a bit differently to picoquant but it should be fine to load. Please could you also send me a non-bidirectional file so I can make sure I'm identifying the headers correctly?

Cheers Sean

AndreZeug commented 5 years ago

Dear Sean, Thanks for addressing this issue. I copied data to the same folder.

Best

Andre

Von: Sean Warren notifications@github.com Gesendet: Mittwoch, 19. September 2018 01:22 An: flimfit/FLIMfit FLIMfit@noreply.github.com Cc: Zeug, Andre Dr. Zeug.Andre@mh-hannover.de; Author author@noreply.github.com Betreff: Re: [flimfit/FLIMfit] FLIMfitFrontEnd (#350)

Hi Andre,

I've had a look at the file, Leica organise their bidirectional data a bit differently to picoquant but it should be fine to load. Please could you also send me a non-bidirectional file so I can make sure I'm identifying the headers correctly?

Cheers Sean

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/flimfit/FLIMfit/issues/350#issuecomment-422591198, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ATVxKpWIs5RRXI4z9q5JKgj4mk8bN9c7ks5ucYARgaJpZM4Vz5xQ.

seanwarren commented 5 years ago

Hi Andre,

Please could yoy try this new version of the FlimReader: https://www.dropbox.com/s/waf2f89s3wilz3o/FlimReader-2018-09-20.zip?dl=0

Many Thanks Sean

AndreZeug commented 5 years ago

Dear Sean, sorry, but have problems downloading. [cid:image001.png@01D45136.57504830] Did I do something wrong?

Best

Andre

Von: Sean Warren notifications@github.com Gesendet: Donnerstag, 20. September 2018 08:33 An: flimfit/FLIMfit FLIMfit@noreply.github.com Cc: Zeug, Andre Dr. Zeug.Andre@mh-hannover.de; Author author@noreply.github.com Betreff: Re: [flimfit/FLIMfit] FLIMfitFrontEnd (#350)

Hi Andre,

Please could yoy try this new version of the FlimReader: https://www.dropbox.com/s/waf2f89s3wilz3o/FlimReader-2018-09-20.zip?dl=0

Many Thanks Sean

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/flimfit/FLIMfit/issues/350#issuecomment-423056951, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ATVxKhB55bfbjVWR_aztOo6U1UwkfsJmks5uczangaJpZM4Vz5xQ.