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mesoSPIM / mesoSPIM-control

Image acquisition software for mesoSPIM light-sheet microscopes.
http://www.mesospim.org
GNU General Public License v3.0
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TIFFs files saved by meso control do not load into MATLAB #68

Closed raacampbell closed 1 year ago

raacampbell commented 1 year ago

The TIFFs are reported in MATLAB as having just one header -- not one header per frame -- and so only the first frame can be loaded. Re-saving them in Fiji allows all frames to be index and therefore loaded.

edit - it also fails if I try to load the images into Elastix.

nvladimus commented 1 year ago

Hi, this is Fiji TIFF, a poorly documented but widely used TIFF format that allows arbitrarily large files. Fiji opens them without problems, correct?

I also added BigTIFF support in the latest release (now on master branch), you may try this one if you have troubles with Fiji TIFFs.

raacampbell commented 1 year ago

It does, yes, but nothing else does. Is there no other bigtiff support? Otherwise I'm not sure the saved TIFFs are that helpful.

On Tue, Nov 15, 2022 at 9:24 AM Nikita Vladimirov @.***> wrote:

Hi, this is Fiji TIFF, a poorly documented but widely used TIFF format that allows arbitrarily large files. Fiji opens them without problems, correct?

I also added BigTIFF support in the latest release (now on master branch), you may try this one if you have troubles with Fiji TIFFs.

— Reply to this email directly, view it on GitHub https://github.com/mesoSPIM/mesoSPIM-control/issues/68#issuecomment-1315026255, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABJNEYYT3DHU2YLL5O5IRZDWINJD5ANCNFSM6AAAAAAR75IZDA . You are receiving this because you authored the thread.Message ID: @.***>

-- Rob Campbell Advanced Microscopy Facility Manager Sainsbury Wellcome Centre, UCL https://www.sainsburywellcome.org/web/content/advanced-microscopy

nvladimus commented 1 year ago

Again, there is an option to save directly in BigTIFF (.btf) files - give it a try.

nvladimus commented 1 year ago

BTW, Imaris, BioFormats and python tifffile also read these Fiji TIFF files with no issues.

raacampbell commented 1 year ago

OK, I will try.

On Tue, Nov 15, 2022 at 10:59 AM Nikita Vladimirov @.***> wrote:

BTW, Imaris, BioFormats and python tifffile also read these Fiji TIFF files with no issues.

— Reply to this email directly, view it on GitHub https://github.com/mesoSPIM/mesoSPIM-control/issues/68#issuecomment-1315142567, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABJNEY3ZVGMSJGXHRP4G4TTWINUH3ANCNFSM6AAAAAAR75IZDA . You are receiving this because you authored the thread.Message ID: @.***>

-- Rob Campbell Advanced Microscopy Facility Manager Sainsbury Wellcome Centre, UCL https://www.sainsburywellcome.org/web/content/advanced-microscopy

nvladimus commented 1 year ago

Matlab tiffReadVolume should be able to read this as well: https://ch.mathworks.com/help/images/ref/tiffreadvolume.html

raacampbell commented 1 year ago

Nice, I didn't know about that. I will test it out.

On Tue, Nov 15, 2022 at 2:30 PM Nikita Vladimirov @.***> wrote:

Matlab tiffReadVolume should be able to read this as well: https://ch.mathworks.com/help/images/ref/tiffreadvolume.html

— Reply to this email directly, view it on GitHub https://github.com/mesoSPIM/mesoSPIM-control/issues/68#issuecomment-1315390930, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABJNEY4U4WSALAENTBJNTUDWIOM6PANCNFSM6AAAAAAR75IZDA . You are receiving this because you authored the thread.Message ID: @.***>

-- Rob Campbell Advanced Microscopy Facility Manager Sainsbury Wellcome Centre, UCL https://www.sainsburywellcome.org/web/content/advanced-microscopy