[Chimera-users] Opening Amira segmentations

[Paul Korir]

Thanks, Tom. I'm delighted at this news.

I'll work hard to make sure these tools are ready in January.

Kind regards,

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 06/12/2019 19:36, Tom Goddard wrote:
> 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 
>> <mailto: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 at 
>> 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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