[ome-devel] Reading HDF files from IMOD and (EMAN2 and chimera)

[David Gault (Staff)]

Hi Tom,

Thank you for providing the info for the Chimera HDF5 spec.
I have added the link to the card (https://trello.com/c/XotYVCqp/43-imod-hdf), we should now have enough information for our initial investigation but I will get in touch if there is any further questions.

With Thanks,
David Gault

On 7 Oct 2016, at 00:42, Tom Goddard <goddard at sonic.net<mailto:goddard at sonic.net>> wrote:

Hi David,

  There is info on the Chimera HDF5 3d image format in the comments at the top of the Python code that reads these file.

http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/libs/VolumeData/cmap/cmap_format.py

  Tom Goddard
  Chimera developer


On Oct 6, 2016, at 6:44 AM, David Gault (Staff) <d.gault at dundee.ac.uk<mailto:d.gault at dundee.ac.uk>> wrote:

Hi David,

Thank you for for bringing this to our attention and providing sample files for testing.
I have created a card on our Trello New Formats board to keep track of the information provided. If there is any further information which we are missing or you feel would be relevant please do let us know.
https://trello.com/c/XotYVCqp/43-imod-hdf

With Thanks,
David Gault

On 3 Oct 2016, at 21:24, David Mastronarde <mast at colorado.edu<mailto:mast at colorado.edu>> wrote:

Hi,

Following up on my correspondence with Jason about HDF files produced by IMOD, there are examples the BioFormats does not read fully or correctly here:

http://bio3d.colorado.edu/private/bernard

ivem1M-sec.hdf is a stack of images, which is what IMOD makes by default when making an HDF file
BioFormats reads only the first image

ivem1M-chunk.hdf is a 3D volume that happens to have data in chunks
ivem1M-pyr.hdf is an image pyramid with 3 volumes in it

chimer.hdf is a volume produced by chimera

eman2.hdf is a small stack of images from older EMAN2
mask.hdf is a volume from contemporary EMAN2
m4160_ptcls.hdf is a stack of images from contemporary EMAN2

All these other things give exceptions.

David
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