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Hi Tom,
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<div class="">Thank you for providing the info for the Chimera HDF5 spec. </div>
<div class="">I have added the link to the card (<a href="https://trello.com/c/XotYVCqp/43-imod-hdf" class="">https://trello.com/c/XotYVCqp/43-imod-hdf</a>), we should now have enough information for our initial investigation but I will get in touch if there
is any further questions.</div>
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<div class="">With Thanks,</div>
<div class="">David Gault</div>
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<blockquote type="cite" class="">
<div class="">On 7 Oct 2016, at 00:42, Tom Goddard <<a href="mailto:goddard@sonic.net" class="">goddard@sonic.net</a>> wrote:</div>
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Hi David,
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<div class=""> There is info on the Chimera HDF5 3d image format in the comments at the top of the Python code that reads these file.</div>
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<div class=""><span class="Apple-tab-span" style="white-space:pre"></span><a href="http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/libs/VolumeData/cmap/cmap_format.py" class="">http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/libs/VolumeData/cmap/cmap_format.py</a></div>
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<div class=""> Tom Goddard</div>
<div class=""> Chimera developer</div>
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<div class="">On Oct 6, 2016, at 6:44 AM, David Gault (Staff) <<a href="mailto:d.gault@dundee.ac.uk" class="">d.gault@dundee.ac.uk</a>> wrote:</div>
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Hi David,
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<div class="">Thank you for for bringing this to our attention and providing sample files for testing.</div>
<div class="">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.</div>
<div class=""><a href="https://trello.com/c/XotYVCqp/43-imod-hdf" class="">https://trello.com/c/XotYVCqp/43-imod-hdf</a></div>
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<div class="">With Thanks,</div>
<div class="">David Gault</div>
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<div class="">On 3 Oct 2016, at 21:24, David Mastronarde <<a href="mailto:mast@colorado.edu" class="">mast@colorado.edu</a>> wrote:</div>
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<div class="">Hi,<br class="">
<br class="">
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:<br class="">
<br class="">
<a href="http://bio3d.colorado.edu/private/bernard" class="">http://bio3d.colorado.edu/private/bernard</a><br class="">
<br class="">
ivem1M-sec.hdf is a stack of images, which is what IMOD makes by default when making an HDF file<br class="">
BioFormats reads only the first image<br class="">
<br class="">
ivem1M-chunk.hdf is a 3D volume that happens to have data in chunks<br class="">
ivem1M-pyr.hdf is an image pyramid with 3 volumes in it<br class="">
<br class="">
chimer.hdf is a volume produced by chimera<br class="">
<br class="">
eman2.hdf is a small stack of images from older EMAN2<br class="">
mask.hdf is a volume from contemporary EMAN2<br class="">
m4160_ptcls.hdf is a stack of images from contemporary EMAN2<br class="">
<br class="">
All these other things give exceptions.<br class="">
<br class="">
David<br class="">
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