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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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cannot seem to segment more than 256 (8bit) cells when loading mask with more than this number. #223

Closed FLIMinator closed 8 years ago

FLIMinator commented 8 years ago

Cannot segment more than 255 objects

seanwarren commented 8 years ago

This is a design limitation ; the masks are stored as 8bit ints. How critical is this?

FLIMinator commented 8 years ago

Hey Sean, I have a data set that involves segmenting nuclei and the count often exceeds 256 - more like 500 per image. I'd like to extract cell-wise lifetimes to get intercellular distributions and the plan is to use them in a paper I'm in the process of writing. If its possible to bump the number up to 16bit ints in the near future it would be massively appreciated. I can forsee this limitation becoming a recurring issue with montaged FLIM images/images greater than 256x256/tumors with densly packed cells.

I'm aware this is on your time so feel free to tell me to wait! I was thinking as a quick fix I could convert my sdt data into quadrants and make x4 tiff stacks.

seanwarren commented 8 years ago

Cool I'll have a look into it (who is this by the way?)

seanwarren commented 8 years ago

OK was simpler than expected. Could you test the version below for me please? It would be good if you could check that segmentation file loading/saving also works as expected. If you're loading segmentation files from an external source, make sure they are saved as 16bit or higher tifs!

windows: https://storage.googleapis.com/flimfit-downloads/merge/4.11.1-3-g07c8a94/FLIMfit%204.11.1-3-g07c8a94%20Setup%20x64.exe

mac: https://storage.googleapis.com/flimfit-downloads/latest/4.11.1-3-g07c8a94/FLIMfit_4.11.1-3-g07c8a94_MACI64.zip

FLIMinator commented 8 years ago

Thanks for this Sean,

Sorry late getting back to you, graduated yesterday and went to the pub......

The mask works but when I fit it only fits what appears to be ~ 256 segments. I saved the image as uint16.

Please try the data, using the settings file within, I have provided if you have time. I pulled an old FLIM image from PhD because the data for the paper is over at Crick ( still visit to analyse data there) and I'm back at Imperial. There are exactly 500 labels in this image. See the screenshots I've put in the folder also, they show the segmentation window found 500 regions.

Cheers,

Hugh

On Wed, May 4, 2016 at 11:59 AM, Sean Warren notifications@github.com wrote:

OK was simpler than expected. Could you test the version below for me please? It would be good if you could check that segmentation file loading/saving also works as expected. If you're loading segmentation files from an external source, make sure they are saved as 16bit or higher tifs!

windows: https://storage.googleapis.com/flimfit-downloads/merge/4.11.1-3-g07c8a94/FLIMfit%204.11.1-3-g07c8a94%20Setup%20x64.exe

mac: https://storage.googleapis.com/flimfit-downloads/latest/4.11.1-3-g07c8a94/FLIMfit_4.11.1-3-g07c8a94_MACI64.zip

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub https://github.com/imperial-photonics/FLIMfit/issues/223#issuecomment-216828506

seanwarren commented 8 years ago

Hi Hugh, no worries. I think I see the problem. Could you send the data to s.warren@garvan.org.au please? Attaching files to github doesn't seem to work by email. I'm thinking to set the limit to 4096 as there are some minor performance implications, does this seem reasonable to you?

seanwarren commented 8 years ago

Hi Hugh, I haven't had time to test the changes but I think this one should work: https://storage.googleapis.com/flimfit-downloads/merge/4.11.1-4-g5aba48f/FLIMfit%204.11.1-4-g5aba48f%20Setup%20x64.exe . Let me know how you get on

FLIMinator commented 8 years ago

Thanks Sean!

That works - I can generate results tables with 500 regions.

Thanks so much for the help/your time. Talk soon.

Cheers,

Hugh

On Fri, May 6, 2016 at 8:46 AM, Sean Warren notifications@github.com wrote:

Hi Hugh, I haven't had time to test the changes but I think this one should work: https://storage.googleapis.com/flimfit-downloads/merge/4.11.1-4-g5aba48f/FLIMfit%204.11.1-4-g5aba48f%20Setup%20x64.exe . Let me know how you get on

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub https://github.com/imperial-photonics/FLIMfit/issues/223#issuecomment-217372570

seanwarren commented 8 years ago

Great, good luck with the paper. Catch you soon

seanwarren commented 8 years ago

This will be released with 4.11.2

FLIMinator commented 8 years ago

Thanks again Sean, see you soon hopefully.

On Fri, May 6, 2016 at 10:22 AM, Sean Warren notifications@github.com wrote:

This will be released with 4.11.2

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub https://github.com/imperial-photonics/FLIMfit/issues/223#issuecomment-217395033