Large multi-image ImageJ tiff file is incorrectly read in as a single plane

[matt.akamatsu@…]

Begin forwarded message:

From: Matthew Akamatsu
Subject: Re: [chimerax-users] Bio-Formats with ChimeraX?
Date: February 7, 2019 at 4:57:24 PM PST
To: Tom Goddard <goddard@…>
Cc: chimerax-users@…

Hi Tom,

Thanks very much for your reply. I am interested in helping out however I can (probably with test use cases) as ChimeraX seems like the best hope to handle and render large 4D-5D optical microscopy data (e.g. the flood of data coming from lattice light sheet microscopes). So far I have noticed that if I try to open a TIFF hyperstack larger than ~3GB it opens as a single plane instead, even if I increase the dataCacheSize to 15000-25000 MB on my 32GB RAM machine with a fast SSD drive (reads at 2.5 GB/s). I tried saving the file in other TIF based formats like ome TIFF and have not had any luck. I am happy to try to share an example file, or take any other suggestions you have for other formats I should try to save the movies as before loading them into ChimeraX.

Matt