[3dem] How to merge tif-files into an *.mrc-file

Fri Apr 7 09:25:50 PDT 2017

Dear Charlotte:

An easy way to do this is in EMAN2,

for i in seriesname*.tif

do e2proc2d.py ${i} new-stack.mrcs  #default behaviour is to append to the stack

done

mv new-stacks.mrcs new-stack.mrc     (or new-stack.st)

The reason for the mrcs extension is that EMAN2 thinks about mrc STACK (.mrcs) and mrc single image (.mrc) files separately based on file extension, even though an mrcs renamed to mrc is read fine by all the other software.

Note that if you do it in EMAN2 the default will be to output the data as floating point unless you tell it not to (which is not a problem for your subsequent processing in this case, but just FYI).

As for how to do it in IMOD, I haven't used tif2mrc so I can't comment on your particular error, but if you are only able to create single image mrc, you can just combine them with newstack afterward, i.e.

for i in seriesname*.tif

do j=`basename ${i} .tif`

tif2mrc ${i} ${j}.mrc

done

newstack seriesname*.mrc new-stack.mrc

rm seriesname*.mrc

Cheers,
Jason

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Today's Topics:

   1. Re: How to merge tif-files into an *.mrc-file
      (Charlotte Hamngren Blomqvist)

----------------------------------------------------------------------

Message: 1
Date: Fri, 7 Apr 2017 12:46:51 +0000
From: Charlotte Hamngren Blomqvist
        <charlotte.hamngren.blomqvist at chalmers.se>
To: "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
Subject: Re: [3dem] How to merge tif-files into an *.mrc-file
Message-ID: <524F2E26-A5B4-490B-80A7-15F1BF4F2FF6 at chalmers.se>
Content-Type: text/plain; charset="utf-8"

Hello again,

I have some questions about the tf2mrc command which is a part of the iMOD package. The specifications say this:

NAME
       tif2mrc - Make a MRC file from TIFF image files.

SYNOPSIS
       tif2mrc [options]  TIFF_input_files...  MRC_output_file

DESCRIPTION
       tif2mrc takes a series of TIFF files and converts them into an MRC
       stack.  tif2mrc can also convert a single multi-page TIFF file to an
       MRC stack.
                             ?.

I have 67 files named: seriesname_001.tif to seriesname_067.tif. How do I write for creating the mrc file? I tried writing in the file names of all the files at the ?TIFF_input_files... ?-position, but it only seem to accept one name at the position. I also tried using the ?cat? command for creating a tiff-stack of the images and then the mrc-file, but the resulting mrc-file is very small and doesn?t open in inspect3D.

Does this ring a bell?

Best,
Charlotte

Fr?n: 3dem <3dem-bounces at ncmir.ucsd.edu> p? uppdrag av Charlotte Hamngren Blomqvist <charlotte.hamngren.blomqvist at chalmers.se>
Datum: fredag 7 april 2017 11:01
Till: Sacha De Carlo <sachadecarlo at yahoo.com>, "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
?mne: Re: [3dem] How to merge tif-files into an *.mrc-file in Inspect3D

Sounds like a good idea.
I will try the tif2mrc command.

Thanks!
/Charlotte

Fr?n: Sacha De Carlo <sachadecarlo at yahoo.com>
Datum: fredag 7 april 2017 10:57
Till: Charlotte Hamngren Blomqvist <charlotte.hamngren.blomqvist at chalmers.se>, "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
?mne: Re: [3dem] How to merge tif-files into an *.mrc-file in Inspect3D

Why not use imod or em2em to convert your tif files into an MRC stack that can then be imported into inspect 3D?

Best
Sacha

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On Friday, April 7, 2017, 10:41 AM, Charlotte Hamngren Blomqvist <charlotte.hamngren.blomqvist at chalmers.se> wrote:

Dear Hivemind,

I want to use computer-generated projections in order to quantify our ET method. Now I want to load the projected images (tif) into the software using the concert/merge files option. I get the error message: "Operation failed Reason: Error reading file". What do I need to change in order for this to work? My version is v. 3.0.0.3494REL of Inspect3D.

Best regards

Charlotte Hamngren Blomqvist

_______________________

Charlotte Hamngren Blomqvist, PhD

Researcher

Department of Physics

Eva Olsson group

Chalmers University of Technology

SE-41296 Gothenburg, Sweden

Tel +46-(0)31 772 51 80<tel:+46-31%20772%2051%2080>

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