Hi Shayne, Thanks for the suggestions. I made some example Python code that defines ChimeraX commands to make the colored outline box, the coverslip slab, and a timestamp label. https://rbvi.github.io/chimerax-recipes/lightsheet/lightsheet.html Maybe some improved version of the colored axes and timestamp command will some day go into ChimeraX. I made a feature request for the color axes which I think might be of interest to others. https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7832 Tom
On Oct 19, 2022, at 12:01 PM, Shayne Quinn via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello, I have been using ChimeraX for a few years now for multidimensional cell bio-imaging and cannot thank the team and developers enough for such an amazing program. I am not sure where to ask for other useful tools so I am starting here. These may already exist but I was unsuccessful in finding them in the user guide so my apologies if I missed them.
1) Is there an option to color the different axis for the 'showOutlineBox' feature for volumes? For example box lines in x-blue, y-green and z-red to help keep orientation (I have included a mock version in the attachment)
2) I work specifically with Lattice Light Sheet Data which requires our 3D cells to be placed on glass coverslip that do not show up in the captured data but are useful for referencing orientation. Is there a feature in place already that would allow me to create a mock coverslip. So far I resorted to importing a throwaway volume (Volume 4 in attachment) and made the threshold for a surface ~0, set it to grey, and made it fill the bottom 5 pixels or so, shown in the attachment.
3) Is there a time stamp feature similar to the scale bar function that has already been implemented?
Thank you so much for all the time and effort that has been put in and for creating such an amazing visualization tool!
Cheers, Shayne Quinn <Chimera Session.PNG>_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
