[chimerax-users] How to show fib-sem tomography data as solid volume

Wed May 25 08:43:31 PDT 2022

Hi Edoardo,

I believe what you want is to set all zero-valued voxels to have full
transparency. This can be done via the histogram levels when viewing the
volume as image and "box" mode, for example:

[image: image.png]
Here I have three different levels along the histogram, where the height of
each level (you can drag with the mouse) is the transparency.

In command line this would be like:

volume #1 style image level -25,0 color black level 0,0 color gray level
25,1 color white voxelSize 1

basically, I defined three levels where I assignin this example::
-the voxel value (-25, 0 and 25 respectively)
-the transparency (0, 0 and 1) where 0 means fully transparent and 1 fully
opaque
-the color I want for that level (black, gray, white)

then voxel colors are saturated below and above the min/max levels (-25,25)
and interpolated linearly between each defined level.
(of course, adjust levels accordingly to your dynamic range, black/white
contrast, etc)

Hope this helps!

Best wishes,
Ricardo

--
Ricardo Diogo Righetto

Em qua., 25 de mai. de 2022 às 13:41, Edoardo D Imprima via ChimeraX-users <
chimerax-users at cgl.ucsf.edu> escreveu:

> Dear Tom, dear Elaine,
>
> Thanks a lot to both of you for the prompt and detailed reply. Elaine’s
> tip goes towards what I would like to achieve, however I think the issue is
> how ChimeraX reads the input. I managed to get this rendering with the
> software Dragonfly (attached the screenshot) where somehow the zeros are
> displayed in 3D as “empty space”. In ChimeraX though they are displayed as
> black pixels. I also adapted your command line Tom (*volume #1 style
> image region 120,0,0,1346,1400,1449 step 1,1,1 colormode l16 proj 2d-z
> showOutlineBox true outlineBoxRgb white*) and I still get the similar
> output (please see attached a snapshot). I converted the input .tiff frames
> as a single .mrc volume (header reports map mode=0) but the issue still
> persists.
>
> Do you have further suggestions?
> I am using ChimeraX (version 1.4rc202205200050 (2022-05-20)) on a windows
> desktop.
>
> Thank you,
>
> Edoardo
>
>
> ------------------------------------------------------
> Dr. Edoardo D'Imprima
> Postdoctoral fellow
> Structural and Computational Biology Unit
> EMBL Heidelberg - Mahamid Group
> Meyerhofstraße 1
> 69117 Heidelberg
> Germany
>
> Phone: +49 6221 387-8531
>
>
> On 24. May 2022, at 19:28, Tom Goddard <goddard at sonic.net> wrote:
>
> Hi Edoardo,
>
>   Elaine's example shows how to make the middle solid box image of your
> figure.  To make the left image which shows 4 slices you can do something
> like this
>
> open 11638 from emdb
> set bgColor white
> volume #1 style image region 0,0,50,256,256,200 step 1,1,50 colormode l8
> proj 2d-z showOutlineBox true outlineBoxRgb black
>
> Here's an explanation of the options in that long volume command.  "style
> image" means gray scale rendering instead of surface.  "region
> 0,0,50,256,256,200" gives the bounds of the region and says to start at z
> plane 50 and end at z plane 200, the six values
> xmin,ymin,zmin,xmax,ymax,zmax.  The "step 1,1,50" means show every voxel
> along x and y axes, but only every 50th plane in z.  The "colormode l8"
> means make the planes opaque. The "proj 2d-z" means show the planes of the
> volume as 2d planes perpendicular to the z axis.  The "showOutlineBox true"
> means to draw the lines outlining the data and "outlineBoxRgb black" makes
> the line color black.  Documentation here
>
> https://www.cgl.ucsf.edu/chimerax/docs/user/commands/volume.html#dispsolid
>
>   A simpler approach would be just to use the Volume Viewer panel and set
> the style (menu above the histogram) to "plane".  That will show a
> scrollbar that lets you flip through the planes (you may have to scroll the
> volume viewer panel to see the horizontal scrollbar below the histogram).
> Then without rotating you just choose the planes you want and save an image
> of each plane with background transparency ("save plane1.png width 1500
> transparent true") and stack them in photo editing program.
>
> Tom
> <emd11638_planes.png>
>
>
> On May 24, 2022, at 9:18 AM, Elaine Meng via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
>
> Hi Edoardo,
> I believe you can do this by choosing "box" display from the rightmost
> pulldown in the Volume Viewer dialog.  See the screenshot attached below.
>
> Volume Viewer dialog settings:
> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/volumeviewer.html>
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> <Screen Shot 2022-05-24 at 9.15.15 AM.png>
>
>
> On May 24, 2022, at 8:00 AM, Edoardo D Imprima via ChimeraX-users
> <chimerax-users at cgl.ucsf.edu> wrote:
>
> Hello,
> Could you please tell me how to display fib-sem tomography data as a
> compact volume that can be navigated by sliding planes? The data consists
> of a series of frames that I can convert as .mrc volume or .mrcs stack. I
> attach a snapshot taken from a review that illustrates (middle panel)
> the visualisation I would like to obtain. The medical-image panel in
> ChimeraX is very handy however, the “full” option shows the volume while I
> need to display the planes of each side to slice through them.
> Looking forward to your feedback,
> Best wishes,
> Edoardo
>
>
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