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<p>Shameless plug but as part of sfftk we use ahds to read Amira
files. It's still in development but the more hands involved the
better it will get at handling Amira files. It's supposed to be
able to read any type (AmiraMesh, HxSurface) but it's as good as
the examples we have.</p>
<p>Install it from PyPI with <span id="pip-command">pip install
ahds==0.2.2.dev0 for the latest release that supports Python
2.7, 3.5, 3.6, 3.7. Checkout the documentation at
<a class="moz-txt-link-freetext" href="https://ahds.readthedocs.io/en/v0.2.0.dev0/overview.html#overview">https://ahds.readthedocs.io/en/v0.2.0.dev0/overview.html#overview</a><br>
</span></p>
<p><span id="pip-command">It also has an API for integration into
other apps.</span></p>
<pre class="moz-signature" cols="72">Paul K. Korir, PhD
3D Visualisation Lead
CS3DB
EMBL-EBI
01223494422
I'm sorry I will only be able to respond to emails after 1300 hrs.
For urgent matters please ring me on the above extension.</pre>
<div class="moz-cite-prefix">On 05/12/2019 20:04, Tom Goddard wrote:<br>
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<blockquote type="cite"
cite="mid:F7E20DD0-4F4D-4FD5-85D7-66617AB79C68@sonic.net">
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Unfortunately Chimera does not handle Amira segmentation files.
Maybe we can add that to ChimeraX or next generation program.
What kind of segmentations do you have? Are they surfaces? Or
are the per-voxel index maps?
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<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div>
<div class=""><br class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On Dec 5, 2019, at 12:02 PM, Guo, Wangbiao
<<a href="mailto:wangbiao.guo@yale.edu" class=""
moz-do-not-send="true">wangbiao.guo@yale.edu</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<div class=""><span style="caret-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; -webkit-text-stroke-width: 0px;
text-decoration: none; float: none; display: inline
!important;" class="">Thank you, Tom. So, what kind of
Amira segment files can I open with Chimera?</span><br
style="caret-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; -webkit-text-stroke-width: 0px;
text-decoration: none;" class="">
<br style="caret-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; -webkit-text-stroke-width: 0px;
text-decoration: none;" class="">
<blockquote type="cite" style="font-family: Helvetica;
font-size: 12px; font-style: normal; font-variant-caps:
normal; font-weight: normal; letter-spacing: normal;
orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; text-decoration: none;"
class="">On Dec 5, 2019, at 3:00 PM, Tom Goddard <<a
href="mailto:goddard@sonic.net" class=""
moz-do-not-send="true">goddard@sonic.net</a>>
wrote:<br class="">
<br class="">
The error message says your Amira file does not contain
BoundingBox in the header. That line tells ChimeraX the
size of the 3D image data in the file. I suspect it
means your Amira file does not contain 3D image data
(instead it might have segmentation surfaces or some
other Amira objects). The Chimera Amira reader only
handles 3d image data.<br class="">
<br class="">
<span class="Apple-tab-span" style="white-space: pre;"> </span>Tom<br
class="">
<br class="">
<br class="">
<blockquote type="cite" class="">On Dec 5, 2019, at
11:36 AM, Guo, Wangbiao <<a
href="mailto:wangbiao.guo@yale.edu" class=""
moz-do-not-send="true">wangbiao.guo@yale.edu</a>>
wrote:<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<Screen Shot 2019-12-05 at 2.32.48 PM.png><br
class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
Hi:<br class="">
When I open my Amira label file by Chimera, I always
come out with an error: cannot find “bounding box”
line, can u help me to figure out?<br class="">
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