<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Jesse,<div class=""><br class=""></div><div class=""> The segmentation surfaces are not very smooth because they are just contour surfaces on the one/zero mask so they show stair steps. I've added an option to the "segmentation surfaces" command to smooth those surfaces, in tomorrow's ChimeraX daily build and 1.5 release candidate.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>segmentation surfaces #1 smooth true</div><div class=""><br class=""></div><div class=""> Tom</div><div class=""><br class=""></div><div class="">Unsmoothed versus smoothed segmentation surfaces</div><div class=""><br class=""></div><div class=""><img apple-inline="yes" id="FAEED676-E6AB-4D0C-99E8-EA5A22C38DF7" width="388" height="389" src="cid:1EE8974C-6D60-4554-99E1-D25269239E55" class=""><img apple-inline="yes" id="0E150065-396F-4171-9D3C-E1498421C3CF" width="388" height="389" src="cid:BD267ABF-75C9-4041-8843-60BE9F70F341" class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Oct 25, 2022, at 12:29 AM, Jesse HANSEN <<a href="mailto:jesse.hansen@ist.ac.at" class="">jesse.hansen@ist.ac.at</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta charset="UTF-8" class=""><div id="divtagdefaultwrapper" dir="ltr" style="font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-size: 12pt; font-family: Calibri, Helvetica, sans-serif;" class=""><div style="margin-top: 0px; margin-bottom: 0px;" class="">hi,</div><div style="margin-top: 0px; margin-bottom: 0px;" class="">thank you, this is a very helpful response! Using segmentation surface #1 each segment I indeed did get all of the surfaces segmented. The problem though is that the segmentation was not very smooth so I'd like to now smooth the surfaces in chimeraX.<br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">As a workaround to directly smoothing the surface, I used segmentation color to color the tomogram volume, which seems to have colored as expected. then I tried "volume splitbyzone #1.2" (for tomogram #1 it has by default #1.1 for surface and #1.2 for image(volume)). This appears to have executed but I do not get any output sub-volumes separated by color. <span class="Apple-converted-space"> </span><br class=""></div><div class=""><br class=""></div><div class="">thanks again</div><div class=""><br class=""></div><div class="">Jesse<br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div></div><hr tabindex="-1" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; display: inline-block; width: 675.21875px;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class=""></span><div id="divRplyFwdMsg" dir="ltr" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><font face="Calibri, sans-serif" style="font-size: 11pt;" class=""><b class="">From:</b><span class="Apple-converted-space"> </span>Tom Goddard <<a href="mailto:goddard@sonic.net" class="">goddard@sonic.net</a>><br class=""><b class="">Sent:</b><span class="Apple-converted-space"> </span>Monday, October 24, 2022 8:32:35 PM<br class=""><b class="">To:</b><span class="Apple-converted-space"> </span>Jesse HANSEN<br class=""><b class="">Cc:</b><span class="Apple-converted-space"> </span><a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a><br class=""><b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [chimerax-users] segmented tomogram density in chimeraX</font><div class=""> </div></div><div style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">Hi Jesse,<div class=""><br class=""></div><div class=""> I guess your segmentation has assigned an integer region number to each grid point. It sounds like those region numbers range from 240 to 250. Displaying that as if is a density map with contour surfaces isn't very useful as you point out. Instead you can use the ChimeraX segmentation command to make a surface for each region, for example</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space: pre;"></span>segmentation surface #1 each segment</div><div class=""><br class=""></div><div class="">where "#1" is the id of the segmentation model you opened, and the "each segment" part says to make a separate surface for each region instead of one surface that includes all regions, Documentation is here</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space: pre;"></span><a href="https://www.cgl.ucsf.edu/chimerax/docs/user/commands/segmentation.html" class="">https://www.cgl.ucsf.edu/chimerax/docs/user/commands/segmentation.html</a></div><div class=""><br class=""></div><div class="">You can also color your tomogram using the segmented regions using the "segmentation color" command. There are examples of both commands for segmented neurons in a rat brain here</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space: pre;"></span><a href="https://www.rbvi.ucsf.edu/chimerax/data/layer4-june2020/mousebrain.html" class="">https://www.rbvi.ucsf.edu/chimerax/data/layer4-june2020/mousebrain.html</a></div><div class=""><br class=""></div><div class="">This example is a bit fancier than your data in that multiple attributes are associated with each region of the segmentation.</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><div class=""><span id="cid:D0AF92C8-D3D5-402F-84FE-45B0BBB05889"><segmentation.jpg></span><br class=""><div class=""><br class=""><blockquote type="cite" class=""><div class="">On Oct 24, 2022, at 6:46 AM, Jesse HANSEN 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 id="divtagdefaultwrapper" dir="ltr" class="" style="font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-size: 12pt; font-family: Calibri, Helvetica, sans-serif;"><div class="" style="margin-top: 0px; margin-bottom: 0px;">hi all,</div><div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class=""></div><div class="" style="margin-top: 0px; margin-bottom: 0px;">I have segmented a tomogram in Amira and exported to chimera for visualization. I first opened the .rec file in chimera and re-saved as .mrc. Okay, the segmentation output gives a<span class="Apple-converted-space"> </span><span class="">fully filled</span><span class="Apple-converted-space"> </span>volume cube except for the regions of segmentation. Obviously things are inverted. Also, the volume viewer shows clear sharp peaks (delta functions) rather than continuous density, as volume slider moves to the right new segmentation features appear. So I used volume filter with "scale" to -1, and I turned off "displayed subregions only". This fixed the inversion problem and now as I slide toward the right I see more segmented densities. However the threshold values are all negative (-250 on the far left to -240 on the far right). This, combined with the densities being sharp peaks, makes it impossible to use this volume like a regular volume for surface coloring, filtering, segger, etc. Any suggestion on how to go from this step to a usable density would be appreciated.</div><div class=""><br class=""></div><div class="">thanks!<br class=""></div><div class="" style="margin-top: 0px; margin-bottom: 0px;">Jesse<br class=""></div><div id="Signature" class=""><div id="divtagdefaultwrapper" dir="ltr" class="" style="font-size: 12pt; font-family: Calibri, Helvetica, sans-serif, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols;"><p class="" style="margin-top: 0px; margin-bottom: 0px;"></p><div class="" style="font-family: Tahoma, serif, EmojiFont; font-size: 13px;"><font size="1" class="" style="font-family: Helvetica, serif, EmojiFont;"><span class="" style="font-size: 12px;">=================================</span></font></div><div class="" style="font-family: Tahoma, serif, EmojiFont; 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