<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Ricardo's suggest is good. Here are a few additional points. The "colormode l8" option I suggested will make the volume planes completely opaque even if you specify transparency as Ricardo suggested. I suggested "colormode l8" because I thought you wanted opaque planes based on the example figure you showed. You should leave out that option for Ricardo's suggestion to work. But if you leave it out then the non-zero part of the data will also be partly transparent and that may not be the appearance you want. The transparency goes from 100% to 0% as the yellow curve on the histogram rises from the bottom to the top. If you wanted completely opaque planes for the positive image values you might use levels like<div class=""><br class=""></div><div class="">volume #1 style image level 0.001,1 color black level 25,1 color white</div><div class=""><br class=""></div><div class="">Because no levels are specified below 0.001 in this command, all of the pixels below that intensity level will not be shown (100% transparent).</div><div class=""><br class=""></div><div class="">It may be that you want to see negative and positive intensity levels but not 0 levels because the negative levels have interesting content. Using 0 to indicate "outside the data" is a really bad choice if both negative and positive levels are important. But you can still handle it by making a notch filter yellow curve that drops to zero just at the value 0.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div class=""><br class=""><div class=""><div><br class=""><blockquote type="cite" class=""><div class="">On May 25, 2022, at 8:43 AM, Ricardo Righetto via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class="">Hi Edoardo,</div><div class=""><br class=""></div><div class="">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 class=""><br class=""><span id="cid:ii_l3lr3nun3"><image.png></span><br class=""></div><div class="">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 class=""><br class=""></div><div class="">In command line this would be like:<br class=""><br class="">volume #1 style image level -25,0 color black level 0,0 color gray level 25,1 color white voxelSize 1<br class=""><br class=""></div><div class="">basically, I defined three levels where I assignin this example:: <br class=""></div><div class="">-the voxel value (-25, 0 and 25 respectively)<br class=""></div><div class="">-the transparency (0, 0 and 1) where 0 means fully transparent and 1 fully opaque<br class=""></div><div class="">-the color I want for that level (black, gray, white)<br class=""><br class=""></div><div class="">then voxel colors are saturated below and above the min/max levels (-25,25) and interpolated linearly between each defined level.</div><div class="">(of course, adjust levels accordingly to your dynamic range, black/white contrast, etc)<br class=""><br class=""></div><div class="">Hope this helps!</div><div class=""><br class=""></div><div class="">Best wishes,</div><div class="">Ricardo<br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><div class=""><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><br class="">--<br class="">Ricardo Diogo Righetto<br class=""></div></div><br class=""></div></div><br class=""><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" class="">chimerax-users@cgl.ucsf.edu</a>> escreveu:<br class=""></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;" class="">Dear Tom, dear Elaine,<div class=""><br class=""></div><div class="">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 class="">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 class=""><br class=""></div><div class="">Do you have further suggestions?</div><div class="">I am using ChimeraX (version 1.4rc202205200050 (2022-05-20)) on a windows desktop. </div><div class=""><br class=""></div><div class="">Thank you,</div><div class=""><br class=""></div><div class="">Edoardo</div><div class=""><br class=""></div><div class=""><span id="cid:180fbd8df3c4de7f5331"><dragonfly_regions.jpg></span><span id="cid:180fbd8df3c8ee060f02"><chimerax_regions_03.PNG></span><br class=""><div class="">
<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;" class="">------------------------------------------------------<br class="">Dr. Edoardo D'Imprima<br class="">Postdoctoral fellow<br class="">Structural and Computational Biology Unit<br class="">EMBL Heidelberg - Mahamid Group<br class="">Meyerhofstraße 1<br class="">69117 Heidelberg<br class="">Germany<br class=""><br class="">Phone: +49 6221 387-8531<br class=""></div><span 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;" class=""></span><br class=""><span class=""><span id="cid:180fbd8df3da74a111b3"><image.jpeg></span></span>
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<div class=""><br class=""><blockquote type="cite" class=""><div class="">On 24. May 2022, at 19:28, Tom Goddard <<a href="mailto:goddard@sonic.net" target="_blank" class="">goddard@sonic.net</a>> wrote:</div><br class=""><div class=""><div style="overflow-wrap: break-word;" class="">Hi Edoardo,<div class=""><br class=""></div><div class=""> 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 class=""><br class=""></div><div class=""><span style="white-space:pre-wrap" class=""> </span>open 11638 from emdb</div><div class=""><span style="white-space:pre-wrap" class=""> </span>set bgColor white</div><div class=""><span style="white-space:pre-wrap" class=""> </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 class=""><div class=""><br class=""></div><div class="">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 class=""><br class=""></div><div class=""><span style="white-space:pre-wrap" class=""> </span><a href="https://www.cgl.ucsf.edu/chimerax/docs/user/commands/volume.html#dispsolid" target="_blank" class="">https://www.cgl.ucsf.edu/chimerax/docs/user/commands/volume.html#dispsolid</a></div><div class=""><br class=""></div><div class=""> 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 class=""><br class=""></div><div class=""><span style="white-space:pre-wrap" class=""> </span>Tom</div><div class=""><span id="gmail-m_-2263549330770868136cid:24A30FA5-8A4A-4517-8333-E2DFDA644E67" class=""><emd11638_planes.png></span></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><blockquote type="cite" class=""><div class="">On May 24, 2022, at 9:18 AM, Elaine Meng via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" target="_blank" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:</div><br class=""><div class=""><div style="overflow-wrap: break-word;" class="">Hi Edoardo,<div class="">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 class=""><br class=""></div><div class="">Volume Viewer dialog settings:</div><div class=""><<a href="https://rbvi.ucsf.edu/chimerax/docs/user/tools/volumeviewer.html" target="_blank" class="">https://rbvi.ucsf.edu/chimerax/docs/user/tools/volumeviewer.html</a>></div><div class=""><br class=""></div><div class="">I hope this helps,</div><div class="">Elaine<br class=""><div class="">-----<br class="">Elaine C. Meng, Ph.D. <br class="">UCSF Chimera(X) team<br class="">Department of Pharmaceutical Chemistry<br class="">University of California, San Francisco<br class=""><br class=""><span id="gmail-m_-2263549330770868136cid:6F591EDD-D8FE-45A5-893A-75D127430A95@gateway.sonic.net" class=""><Screen Shot 2022-05-24 at 9.15.15 AM.png></span><br class=""><br class=""></div><br class=""><blockquote type="cite" class="">On May 24, 2022, at 8:00 AM, Edoardo D Imprima via ChimeraX-users <chimerax-<a href="mailto:users@cgl.ucsf.edu" target="_blank" class="">users@cgl.ucsf.edu</a>> wrote:<br class=""><br class="">Hello,<br class="">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 class="">Looking forward to your feedback,<br class="">Best wishes,<br class="">Edoardo<br class=""></blockquote><br class=""></div></div>_______________________________________________<br class="">ChimeraX-users mailing list<br class=""><a href="mailto:ChimeraX-users@cgl.ucsf.edu" target="_blank" class="">ChimeraX-users@cgl.ucsf.edu</a><br class="">Manage subscription:<br class=""><a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" target="_blank" class="">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a><br class=""></div></blockquote></div><br class=""></div></div></div></blockquote></div><br class=""></div></div>_______________________________________________<br class="">
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