Hi J,

  Thanks for your nice comments about ChimeraX.  It uses the Python tifffile module (https://pypi.org/project/tifffile/) to open TIFF files developed by Christoph Gohlke specifically for light microscopy and that can handle BigTIFF format which is needed since original TIFF only has a maximum size of 4 GB.

  As a test I made a 6 Gbyte 3d random image and opened it in ChimeraX 1.10 without any trouble.  I made the example file in Python with this code

    import numpy, tifffile
    data = numpy.random.randint(0, 255, (2000, 1000, 1000, 3), 'uint8')
    tifffile.imwrite('/Users/goddard/Desktop/temp.tif', data, bigtiff=True, photometric='rgb')

then opened it with ChimeraX command

open temp.tif

Can you show me an example where it doesn't work?

Tom

2k x 1k x 1k random BigTIFF image in ChimeraX
bigtiff.png

On Jul 16, 2025, at 5:32 PM, José Jorge Ramírez Franco via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi there,

First of all, thank you for this outstanding piece of software. ChimeraX is truly invaluable and has become an essential tool in my workflow.

As a microscopist working primarily with light microscopy (particularly confocal and light-sheet imaging) I’ve found ChimeraX’s rendering capabilities to be far superior to most tools currently available. I’ve even recommended its use several times on the image.sc forum, especially for rendering high-quality visualizations.

In fact, I recently noticed that there was no #chimerax tag on the forum (surprisingly!) so I took the liberty of creating one. You can find the related post here:

https://forum.image.sc/t/3d-multichannel-surface-rendering-from-z-stacks-napari-script-and-fiji-alternatives/114771/4?u=j_ramirez

While I have this opportunity, I’d like to suggest a feature that I believe would significantly enhance ChimeraX’s utility for large-scale light-sheet microscopy datasets: support for .tiff files larger than 4 GB. 

These large file sizes are quite common in light-sheet acquisitions, and the ability to open them natively in ChimeraX would be a substantial benefit to researchers in this field.

Thank you once again for all the incredible work that goes into developing and maintaining ChimeraX. It’s deeply appreciated.

Warm regards,

J
--
J. Jorge Ramírez-Franco
PhD
Institut de Neurosciences de la Timone, SpiCCI Team
Faculté de Médecine
27, boulevard Jean Moulin
13005 Marseille, France
_______________________________________________
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu
To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu
Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/