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@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@sonic.net <mailto:goddard@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@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? _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fplato.cgl.ucsf.edu%2Fmailman%2Flistinfo%2Fchimera-users&data=02%7C01%7Cwangbiao.guo%40yale.edu%7Ce679ebbb7b8b49c59b6208d779bdc5ff%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637111728315753409&sdata=scrFe9T%2BHwAmaZgA8KEztPdlmaPX35iIex1QcX29LJ4%3D&reserved=0 <https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fplato.cgl.ucsf.edu%2Fmailman%2Flistinfo%2Fchimera-users&data=02%7C01%7Cwangbiao.guo%40yale.edu%7Ce679ebbb7b8b49c59b6208d779bdc5ff%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637111728315753409&sdata=scrFe9T%2BHwAmaZgA8KEztPdlmaPX35iIex1QcX29LJ4%3D&reserved=0>
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@yale.edu <mailto:wangbiao.guo@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@sonic.net <mailto:goddard@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@yale.edu <mailto:wangbiao.guo@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? _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription:https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fplato.cgl.ucsf.edu%2Fmailman%2Flistinfo%2Fchimera-users&data=02%7C01%7Cwangbiao.guo%40yale.edu%7Ce679ebbb7b8b49c59b6208d779bdc5ff%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637111728315753409&sdata=scrFe9T%2BHwAmaZgA8KEztPdlmaPX35iIex1QcX29LJ4%3D&reserved=0
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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@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@yale.edu <mailto:wangbiao.guo@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@sonic.net <mailto:goddard@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@yale.edu <mailto:wangbiao.guo@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? _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fplato.cgl.ucsf.edu%2Fmailman%2Flistinfo%2Fchimera-users&data=02%7C01%7Cwangbiao.guo%40yale.edu%7Ce679ebbb7b8b49c59b6208d779bdc5ff%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637111728315753409&sdata=scrFe9T%2BHwAmaZgA8KEztPdlmaPX35iIex1QcX29LJ4%3D&reserved=0 <https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fplato.cgl.ucsf.edu%2Fmailman%2Flistinfo%2Fchimera-users&data=02%7C01%7Cwangbiao.guo%40yale.edu%7Ce679ebbb7b8b49c59b6208d779bdc5ff%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637111728315753409&sdata=scrFe9T%2BHwAmaZgA8KEztPdlmaPX35iIex1QcX29LJ4%3D&reserved=0>
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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@ebi.ac.uk <mailto:pkorir@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@yale.edu <mailto:wangbiao.guo@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@sonic.net <mailto:goddard@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@yale.edu <mailto:wangbiao.guo@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? _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription:https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fplato.cgl.ucsf.edu%2Fmailman%2Flistinfo%2Fchimera-users&data=02%7C01%7Cwangbiao.guo%40yale.edu%7Ce679ebbb7b8b49c59b6208d779bdc5ff%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637111728315753409&sdata=scrFe9T%2BHwAmaZgA8KEztPdlmaPX35iIex1QcX29LJ4%3D&reserved=0
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participants (2)
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Paul Korir -
Tom Goddard