[Chimera-users] Opening Amira segmentations

Paul Korir pkorir at ebi.ac.uk
Fri Dec 6 02:03:10 PST 2019

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 at 

It also has an API for integration into other apps.

Paul K. Korir, PhD
3D Visualisation Lead

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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