Show volume outline box in with red,green,blue edges for x,y,z axes

[shayne.quinn@…]

Begin forwarded message:

From: Shayne Quinn via ChimeraX-users <chimerax-users@…>
Subject: [chimerax-users] Useful tools ideas/requests
Date: October 19, 2022 at 12:01:13 PM PDT
To: chimerax-users@…
Reply-To: Shayne Quinn

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

[Tom Goddard]

Example of axis colored outline box