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<p>Dear all,</p>
<p>as it seems to be the logical trend now, Scipion also keeps the
movies in the original (compressed or not) format, and decompress
them if necessary on the fly (the gain is also considered after
this decompression). In this way, there is no need for extra
space.</p>
<p>Kind regards, Carlos Oscar<br>
</p>
<div class="moz-cite-prefix">El 29/08/2019 a las 21:35, Ali Punjani
escribió:<br>
</div>
<blockquote type="cite"
cite="mid:CAP_b-V_enQCdtXNkuQxhVDwBEs8+TR_zuTR93pKkuNG40S9XKA@mail.gmail.com">
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<div style="color:rgb(49,49,49);font-size:16px;word-spacing:1px"
dir="auto">
<div dir="auto" style="font-size:1rem">Hi Matthew,</div>
</div>
<div dir="auto"
style="color:rgb(49,49,49);font-size:16px;word-spacing:1px"><br>
</div>
<div dir="auto"
style="color:rgb(49,49,49);word-spacing:1px;font-size:1rem">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>
</div>
<div dir="auto"
style="color:rgb(49,49,49);word-spacing:1px;font-size:1rem"><br>
</div>
<div dir="auto"
style="color:rgb(49,49,49);word-spacing:1px;font-size:1rem">Ali</div>
<div><br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Thu, Aug 29, 2019 at 3:19
PM Matthew H. Cahn <<a href="mailto:mcahn@princeton.edu"
moz-do-not-send="true">mcahn@princeton.edu</a>> wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">
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?
<div><br>
</div>
<div>— Matthew</div>
<div><br>
<div>
<div style="word-wrap:break-word">
<div
style="color:rgb(0,0,0);font-variant-caps:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><font
size="2"><b>|| Matthew Cahn | Linux
Administrator | Dept. of Molecular Biology /
Research Computing | Princeton University |
(609) 258-5404 | <a
href="mailto:mcahn@princeton.edu"
target="_blank" moz-do-not-send="true">mcahn@princeton.edu</a>
||<br>
</b></font><br>
</div>
</div>
</div>
<br>
</div>
</div>
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<pre class="moz-signature" cols="72">--
------------------------------------------------------------------------
Carlos Oscar Sánchez Sorzano e-mail: <a class="moz-txt-link-abbreviated" href="mailto:coss@cnb.csic.es">coss@cnb.csic.es</a>
Biocomputing unit <a class="moz-txt-link-freetext" href="http://i2pc.es/coss">http://i2pc.es/coss</a>
National Center of Biotechnology (CSIC)
c/Darwin, 3
Campus Universidad Autónoma (Cantoblanco) Tlf: 34-91-585 4510
28049 MADRID (SPAIN) Fax: 34-91-585 4506
------------------------------------------------------------------------
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