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<p style="margin-top:0;margin-bottom:0">Dear Yehuda,</p>
<p style="margin-top:0;margin-bottom:0">If I were unstacking mrc stacks to tif, I would probably avoid tif stacks altogether to create one tif per frame. This can be handled smoothly with EMAN2 as follows:<br>
</p>
<p style="margin-top:0;margin-bottom:0">e2proc2d.py input.mrc output.tif --unstacking</p>
<p style="margin-top:0;margin-bottom:0">which would result in files output-01.tif output-02.tif output-03.tif &c &c. You could then compress these tif.</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">If your purpose is to save space, I echo the previous comments about simply (losslessly) compressing the mrc stack. Past lossless compression, if you are collecting with significant oversampling, you can clip your raw
stacks in Fourier space for archiving (lossy but unlikely to affect the utility of the data if done conservatively). You can also truncate the mrc stacks to a lower bitrate after confirming that your raw frames don't have too many counts (lossy if some pixels
are outside the dynamic range of the truncated file).</p>
<p style="margin-top:0;margin-bottom:0">One of the big drivers of disk utilization is users collecting in superres mode by default instead of considering whether it's appropriate for the experiment. In experiments where superres is useful, you can still usually
Fourier clip from 8k * 8k to 6k * 6k without losing anything that matters.<br>
</p>
<p style="margin-top:0;margin-bottom:0">Best,</p>
<p style="margin-top:0;margin-bottom:0">Jason Kaelber</p>
<p style="margin-top:0;margin-bottom:0"></p>
<div>--<br>
J T Kaelber, PhD<br>
Director, Rutgers New Jersey CryoEM/CryoET Core Facility<br>
Institute for Quantitative Biomedicine<br>
174 Frelinghuysen Rd<br>
Piscataway, NJ 08854</div>
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1. Re: [ccpem] Converting MRC to tiff (Marin van Heel)<br>
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----------------------------------------------------------------------<br>
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Message: 1<br>
Date: Sun, 3 Jun 2018 07:18:02 -0300<br>
From: Marin van Heel <marin.vanheel@googlemail.com><br>
To: Yehuda Halfon <yehuda.halfon@WEIZMANN.AC.IL>, CCPEM@JISCMAIL.AC.UK<br>
Cc: "3dem@ncmir.ucsd.edu" <3dem@ncmir.ucsd.edu><br>
Subject: Re: [3dem] [ccpem] Converting MRC to tiff<br>
Message-ID: <3ef6faf6-f85b-dc7c-0228-a5bf4447f8be@googlemail.com><br>
Content-Type: text/plain; charset="windows-1252"; Format="flowed"<br>
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<br>
Dear Yehuda Halfon<br>
<br>
The em2em converter (Image-Science.de) should do the trick but storing <br>
(4-bit/8-bit?) MRC movies in tiff is not a good idea: very few programs <br>
can handle tiff stacks. Moreover if the TIFFs are not compressed you <br>
will not necessarily win any space. You are probably best off using a <br>
standard loss-less compression program ("zip"), and convert them back <br>
when you need it again. You must always keep your original raw data <br>
"forever" in a loss-less form.<br>
<br>
Marin van Heel<br>
<br>
<br>
On 03/06/2018 06:02, Yehuda Halfon wrote:<br>
> Hi there,<br>
><br>
> We have a bunch of MRC movie files the are eating at out storage, and <br>
> since more are coming I was wondering if there is a good way to <br>
> convert them into tiff to save space?<br>
><br>
> I know that the best way is to save them directly as tif from EPU/ <br>
> serialEM and that is what we will to in the future. But we need to <br>
> find a solution to the ones we have now.<br>
><br>
> Thanks,<br>
><br>
> Yehuda Halfon<br>
><br>
> ------------------------------------------------------------------------<br>
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-- <br>
==============================================================<br>
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Prof Dr Ir Marin van Heel<br>
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email: m.vanheel(A_T)imperial.ac.uk<br>
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