Changes between Initial Version and Version 1 of Ticket #8358


Ignore:
Timestamp:
Jan 23, 2023, 11:02:10 AM (3 years ago)
Author:
Tom Goddard
Comment:

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  • Ticket #8358

    • Property Cc pkorir@… added
    • Property Component Unassigned → Volume Data
    • Property Owner set to Tom Goddard
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Reporter changed from goddard@… to martin.schorb@…
    • Property Status new → assigned
    • Property Summary ChimeraX bug report submission → EMDB SFF segmentation file: AttributeError: 'SFFMesh' object has no attribute 'num_vertices'

  • Ticket #8358 – Description

    initial v1  
     1{{{
     2From: Paul Korir
     3Subject: Re: SFF conversion
     4Date: January 20, 2023 at 3:24:17 AM PST
     5To: Tom Goddard
     6Cc: Martin Schorb
     7
     8Hi Tom,
     9
     10Happy new year!
     11
     12Martin (cc'ed) has tried to view an EMDB-SFF file with meshes and is getting an error which I think is an integration issue with reading meshes. Could you please take a look? We have verified that the file is OK (we can view it on our local viewer).
     13
     14This is for ChimeraX version 1.5.
     15
     16The traceback is here: https://pastebin.com/FnVVyNxa
     17
     18I'm am on on hand to help where you need my help.
     19
     20Thanks so much.
     21
     22
     23Paul K. Korir, PhD
     243D Visualisation Lead
     25CS3DB
     26EMBL-EBI
     27
     28On 20/01/2023 10:03, Martin Schorb wrote:
     29Dear Paul,
     30
     31we are working on an EMPIAR submission and like to add our segmentations to the volume.
     32
     33These are in Amira format and I found out that converting the surfaces (surf files) seems to work.
     34However, I am left with two issues:
     35
     36- How to deal with scaling compared to the original volumes as the segmentations were created using binned data? I get a warning when converting with sfftk but do not have the original volume available in a supported format (tif slices only). Can the scaling be done afterwards?
     37
     38- I like to check whether the conversion worked, and the only software to visualize SFF I found was ChimeraX. NOw when trying to load one of the converted files, I end up getting errors: "Attribute Error: 'SFFMEsh object has no attribute 'num_vertices'"
     39
     40thanks for looking into this,
     41Martin
     42}}}
     43
    144{{{
    245The following bug report has been submitted: