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<p>Thanks, Tom. I'm delighted at this news. <br>
</p>
<p>I'll work hard to make sure these tools are ready in January.</p>
<p>Kind regards,<br>
</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 06/12/2019 19:36, Tom Goddard wrote:<br>
</div>
<blockquote type="cite"
cite="mid:75181521-D9A2-443A-9D90-D323A2717C8C@sonic.net">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
Hi Paul,
<div class=""><br class="">
</div>
<div class=""> That's great! I plan to add more segmentation
visualization features to ChimeraX in the coming year including
the new EMDB segmentation file format (probably when sfftk-rw
version 0.8 is out) and it would also be useful to allow
importing Amira segmentations using your ahds PyPi library.
I've made a ChimeraX ticket to track progress on that.</div>
<div class=""><br class="">
</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a
href="https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/2665"
class="" moz-do-not-send="true">https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/2665</a></div>
<div class=""><br class="">
</div>
<div class=""> Tom</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On Dec 6, 2019, at 2:03 AM, Paul Korir <<a
href="mailto:pkorir@ebi.ac.uk" class=""
moz-do-not-send="true">pkorir@ebi.ac.uk</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<meta http-equiv="Content-Type" content="text/html;
charset=UTF-8" class="">
<div class="">
<p class="">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 class="">Install it from PyPI with <span
id="pip-command" class="">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"
moz-do-not-send="true">https://ahds.readthedocs.io/en/v0.2.0.dev0/overview.html#overview</a><br
class="">
</span></p>
<p class=""><span id="pip-command" class="">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 class="">
</div>
<blockquote type="cite"
cite="mid:F7E20DD0-4F4D-4FD5-85D7-66617AB79C68@sonic.net"
class="">
<meta http-equiv="Content-Type" content="text/html;
charset=UTF-8" class="">
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?
<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=""><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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