<div dir="ltr"><div>Hi Edoardo,</div><div><br></div><div>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:<br><br><img src="cid:ii_l3lr3nun3" alt="image.png" width="561" height="138"><br></div><div>Here I have three different levels along the histogram, where the height of each level (you can drag with the mouse) is the transparency.<br><br></div><div>In command line this would be like:<br><br>volume #1 style image level -25,0 color black level 0,0 color gray level 25,1 color white voxelSize 1<br><br></div><div>basically, I defined three levels where I assignin this example:: <br></div><div>-the voxel value (-25, 0 and 25 respectively)<br></div><div>-the transparency (0, 0 and 1) where 0 means fully transparent and 1 fully opaque<br></div><div>-the color I want for that level (black, gray, white)<br><br></div><div>then voxel colors are saturated below and above the min/max levels (-25,25) and interpolated linearly between each defined level.</div><div>(of course, adjust levels accordingly to your dynamic range, black/white contrast, etc)<br><br></div><div>Hope this helps!</div><div><br></div><div>Best wishes,</div><div>Ricardo<br></div><div><br></div><div><br></div><div><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><br>--<br>Ricardo Diogo Righetto<br></div></div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Em qua., 25 de mai. de 2022 às 13:41, Edoardo D Imprima via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu">chimerax-users@cgl.ucsf.edu</a>> escreveu:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div style="overflow-wrap: break-word;">Dear Tom, dear Elaine,<div><br></div><div>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 (<i>volume #1 style image region 120,0,0,1346,1400,1449 step 1,1,1 colormode l16 proj 2d-z showOutlineBox true outlineBoxRgb white</i>) 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. </div><div><br></div><div>Do you have further suggestions?</div><div>I am using ChimeraX (version 1.4rc202205200050 (2022-05-20)) on a windows desktop. </div><div><br></div><div>Thank you,</div><div><br></div><div>Edoardo</div><div><br></div><div><img id="gmail-m_-2263549330770868136D0E209B2-5760-4933-836E-052067A8F0DB" src="cid:180fbd8df3c4de7f5331"><img id="gmail-m_-22635493307708681364CEE1005-843A-4789-891A-670AB06F497C" src="cid:180fbd8df3c8ee060f02"><br><div>
<div style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;color:rgb(0,0,0)">------------------------------------------------------<br>Dr. Edoardo D'Imprima<br>Postdoctoral fellow<br>Structural and Computational Biology Unit<br>EMBL Heidelberg - Mahamid Group<br>Meyerhofstraße 1<br>69117 Heidelberg<br>Germany<br><br>Phone: +49 6221 387-8531<br></div><span style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"></span><br><span><img id="gmail-m_-226354933077086813693B7C8D0-F5B0-46B4-8801-9DAAEA49E144" src="cid:180fbd8df3da74a111b3"></span>
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<div><br><blockquote type="cite"><div>On 24. May 2022, at 19:28, Tom Goddard <<a href="mailto:goddard@sonic.net" target="_blank">goddard@sonic.net</a>> wrote:</div><br><div><div style="overflow-wrap: break-word;">Hi Edoardo,<div><br></div><div> 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</div><div><br></div><div><span style="white-space:pre-wrap"> </span>open 11638 from emdb</div><div><span style="white-space:pre-wrap"> </span>set bgColor white</div><div><span style="white-space:pre-wrap"> </span>volume #1 style image region 0,0,50,256,256,200 step 1,1,50 colormode l8 proj 2d-z showOutlineBox true outlineBoxRgb black<br><div><br></div><div>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</div><div><br></div><div><span style="white-space:pre-wrap"> </span><a href="https://www.cgl.ucsf.edu/chimerax/docs/user/commands/volume.html#dispsolid" target="_blank">https://www.cgl.ucsf.edu/chimerax/docs/user/commands/volume.html#dispsolid</a></div><div><br></div><div> 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.</div><div><br></div><div><span style="white-space:pre-wrap"> </span>Tom</div><div><span id="gmail-m_-2263549330770868136cid:24A30FA5-8A4A-4517-8333-E2DFDA644E67"><emd11638_planes.png></span></div><div><br></div><div><br></div><div><blockquote type="cite"><div>On May 24, 2022, at 9:18 AM, Elaine Meng via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" target="_blank">chimerax-users@cgl.ucsf.edu</a>> wrote:</div><br><div><div style="overflow-wrap: break-word;">Hi Edoardo,<div>I believe you can do this by choosing "box" display from the rightmost pulldown in the Volume Viewer dialog. See the screenshot attached below.</div><div><br></div><div>Volume Viewer dialog settings:</div><div><<a href="https://rbvi.ucsf.edu/chimerax/docs/user/tools/volumeviewer.html" target="_blank">https://rbvi.ucsf.edu/chimerax/docs/user/tools/volumeviewer.html</a>></div><div><br></div><div>I hope this helps,</div><div>Elaine<br><div>-----<br>Elaine C. Meng, Ph.D. <br>UCSF Chimera(X) team<br>Department of Pharmaceutical Chemistry<br>University of California, San Francisco<br><br><span id="gmail-m_-2263549330770868136cid:6F591EDD-D8FE-45A5-893A-75D127430A95@gateway.sonic.net"><Screen Shot 2022-05-24 at 9.15.15 AM.png></span><br><br></div><br><blockquote type="cite">On May 24, 2022, at 8:00 AM, Edoardo D Imprima via ChimeraX-users <chimerax-<a href="mailto:users@cgl.ucsf.edu" target="_blank">users@cgl.ucsf.edu</a>> wrote:<br><br>Hello,<br>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. <br>Looking forward to your feedback,<br>Best wishes,<br>Edoardo<br></blockquote><br></div></div>_______________________________________________<br>ChimeraX-users mailing list<br><a href="mailto:ChimeraX-users@cgl.ucsf.edu" target="_blank">ChimeraX-users@cgl.ucsf.edu</a><br>Manage subscription:<br><a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" target="_blank">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a><br></div></blockquote></div><br></div></div></div></blockquote></div><br></div></div>_______________________________________________<br>
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