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Thanks, Henning. Do any of the commonly-used processing programs (e.g. RELION, CryoSPARC) read or write mrcz format?
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<div class="">Matthew</div>
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<font size="2" class=""><b class="">|| Matthew Cahn | Linux Administrator | Dept. of Molecular Biology / Research Computing | Princeton University | (609) 258-5404 | <a href="mailto:mcahn@princeton.edu" class="">mcahn@princeton.edu</a> ||<br class="">
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<div class="">On Aug 29, 2019, at 5:04 PM, Henning Stahlberg <<a href="mailto:henning.stahlberg@unibas.ch" class="">henning.stahlberg@unibas.ch</a>> wrote:</div>
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<div dir="auto" class="">Hi,
<div class="">Gain corrected images are floating point. Loss-less compression of noisy floats is not trivial. The MRCZ format of Rob McLeod deals with that, see</div>
<div class=""> <a href="https://doi.org/10.1016/j.jsb.2017.11.012" class="">https://doi.org/10.1016/j.jsb.2017.11.012</a></div>
<div class="">Henning. <br class="">
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<div dir="ltr" class="">Henning Stahlberg
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On Aug 29, 2019, at 22:51, Matthew H. Cahn <<a href="mailto:mcahn@princeton.edu" class="">mcahn@princeton.edu</a>> wrote:<br class="">
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<div dir="ltr" class="">By the way, why don’t gain-corrected images compress well? Doesn’t gain-correction just change the dynamic range of the pixels?
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<div class="">Matthew</div>
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<font size="2" class=""><b class="">|| Matthew Cahn | Linux Administrator | Dept. of Molecular Biology / Research Computing | Princeton University | (609) 258-5404 | <a href="mailto:mcahn@princeton.edu" class="">mcahn@princeton.edu</a> ||<br class="">
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<div class="">On Aug 29, 2019, at 3:35 PM, Ali Punjani <<a href="mailto:alipunjani@cs.toronto.edu" class="">alipunjani@cs.toronto.edu</a>> wrote:</div>
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<div dir="auto" style="font-size:1rem" class="">Hi Matthew,</div>
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In cryoSPARC, LZW compressed tiff files are handled natively and decompressed in parallel on the fly as needed. They are never stored in decompressed form, so the original tiff files (created by IMOD, serialEM, etc) are retained throughout a project. This is
a very common workflow, though as noted, for effective tiff compression the movies should not be gain corrected - the gain reference must be stored separately and provided at import time. </div>
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Ali</div>
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<div dir="ltr" class="gmail_attr">On Thu, Aug 29, 2019 at 3:19 PM Matthew H. Cahn <<a href="mailto:mcahn@princeton.edu" class="">mcahn@princeton.edu</a>> wrote:<br class="">
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<div style="word-wrap:break-word" class="">Is it possible to convert mrc files to compressed tiff immediately after data collection, and use that compressed tiff for all the downstream processing? For example, if I compress the mrc files from our Krios to
tiff with LZW (lossless) compression, using IMOD’s mrc2tif, can motioncor2, RELION, CryoSPARC, etc. handle that format and keep everything compressed throughout the process?
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<div class="">— Matthew</div>
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<font size="2" class=""><b class="">|| Matthew Cahn | Linux Administrator | Dept. of Molecular Biology / Research Computing | Princeton University | (609) 258-5404 | <a href="mailto:mcahn@princeton.edu" target="_blank" class="">mcahn@princeton.edu</a>
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