[3dem] Converting MRC to tiff (Marin van Heel)

Sun Jun 3 17:23:47 PDT 2018

Dear Yehuda,

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:

e2proc2d.py input.mrc output.tif --unstacking

which would result in files output-01.tif output-02.tif output-03.tif &c &c. You could then compress these tif.

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).

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.

Best,

Jason Kaelber

--
J T Kaelber, PhD
Director, Rutgers New Jersey CryoEM/CryoET Core Facility
Institute for Quantitative Biomedicine
174 Frelinghuysen Rd
Piscataway, NJ 08854

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Today's Topics:

   1. Re: [ccpem] Converting MRC to tiff (Marin van Heel)

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Message: 1
Date: Sun, 3 Jun 2018 07:18:02 -0300
From: Marin van Heel <marin.vanheel at googlemail.com>
To: Yehuda Halfon <yehuda.halfon at WEIZMANN.AC.IL>, CCPEM at JISCMAIL.AC.UK
Cc: "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
Subject: Re: [3dem] [ccpem] Converting MRC to tiff
Message-ID: <3ef6faf6-f85b-dc7c-0228-a5bf4447f8be at googlemail.com>
Content-Type: text/plain; charset="windows-1252"; Format="flowed"

Dear Yehuda Halfon

The em2em converter (Image-Science.de) should do the trick but storing
(4-bit/8-bit?) MRC movies in tiff is not a good idea: very few programs
can handle tiff stacks. Moreover if the TIFFs are not compressed you
will not necessarily win any space. You are probably best off using a
standard loss-less compression program ("zip"), and convert them back
when you need it again. You must always keep your original raw data
"forever" in a loss-less form.

Marin van Heel

On 03/06/2018 06:02, Yehuda Halfon wrote:
> Hi there,
>
> We have a bunch of MRC movie files the are eating at out storage, and
> since more are coming I was wondering if there is a good way to
> convert them into tiff to save space?
>
> I know that the best way is to save them directly as tif from EPU/
> serialEM and that is what we will to in the future. But we need to
> find a solution to the ones we have now.
>
> Thanks,
>
> Yehuda Halfon
>
> ------------------------------------------------------------------------
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--
==============================================================

     Prof Dr Ir Marin van Heel

     Laborat?rio Nacional de Nanotecnologia - LNNano
     CNPEM/LNNano, Campinas, Brazil

     tel:    +55-19-3518-2316
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--------------------------------------------------
     Emeritus Professor of Cryo-EM Data Processing
     Leiden University
     Mobile NL: +31(0)652736618 (ALWAYS ACTIVE SMS)
--------------------------------------------------
     Emeritus Professor of Structural Biology
     Imperial College London
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--------------------------------------------------

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