[Chimera-users] Opening Amira segmentations

[Tom Goddard]

Hi Paul,

  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.

	https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/2665

  Tom



> On Dec 6, 2019, at 2:03 AM, Paul Korir <pkorir at ebi.ac.uk> wrote:
> 
> 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.
> 
> Install it from PyPI with 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 athttps://ahds.readthedocs.io/en/v0.2.0.dev0/overview.html#overview <https://ahds.readthedocs.io/en/v0.2.0.dev0/overview.html#overview>
> It also has an API for integration into other apps.
> 
> 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.
> On 05/12/2019 20:04, Tom Goddard wrote:
>> 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?
>> 
>> 	Tom
>> 
>> 
>>> On Dec 5, 2019, at 12:02 PM, Guo, Wangbiao <wangbiao.guo at yale.edu <mailto:wangbiao.guo at yale.edu>> wrote:
>>> 
>>> Thank you, Tom. So, what kind of Amira segment files can I open with Chimera?
>>> 
>>>> On Dec 5, 2019, at 3:00 PM, Tom Goddard <goddard at sonic.net <mailto:goddard at sonic.net>> wrote:
>>>> 
>>>> 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.
>>>> 
>>>> 	Tom
>>>> 
>>>> 
>>>>> On Dec 5, 2019, at 11:36 AM, Guo, Wangbiao <wangbiao.guo at yale.edu <mailto:wangbiao.guo at yale.edu>> wrote:
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> <Screen Shot 2019-12-05 at 2.32.48 PM.png>
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> Hi:
>>>>> 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?
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