[chimerax-users] Useful tools ideas/requests

[Shayne Quinn]

Awesome, thank you so much the axes are exactly what I am looking for as
well as the coverslip idea! I realized I was a little unclear on the time
stamp comment. I was wondering if there was something for timestamping
Vseries data to apply a changing timestamp to each frame of a movie.

On Thu, Oct 20, 2022 at 8:12 PM Tom Goddard <goddard at sonic.net> wrote:

> 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 at 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>_______________________________________________
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