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CCPEM  June 2018

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Subject:

Re: Converting MRC to tiff

From:

Takanori Nakane <[log in to unmask]>

Reply-To:

Takanori Nakane <[log in to unmask]>

Date:

Sun, 3 Jun 2018 11:15:36 +0100

Content-Type:

text/plain

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text/plain (76 lines)

Hi,

If it is from K2 and not gain normalised, compression is trivial:
  mrc2tif -s -c zip input.mrcs ouput.tiff (using IMOD)
The output usually becomes less than 5-10 % of the input.
(Of course this depends on the dose rate)

If it is gain-normalised, the file is in 32-bit float and very hard to
compress. You must first divide them by the gain reference to bring it
back to integer and then compress. If you don't have the gain reference,
you can estimate them by a simple program that finds common divisor over
all frames for each pixel. This works fine for data from serial EM.
I could loss-lessly compress EMPIAR-10061 from 12.6 TB to 306 GB
this way. See my old post at 
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1703&L=CCPEM&P=R33113&1=CCPEM.

Unfortunately, EPU (or DM?) seems to do something with 'defect' pixels.
I don't know what is happening here. Their values are not multiples of
the gain reference and the above method is no longer lossless.
But these pixels are defects anyway and probably don't matter.

For images from Falcon III, the data are 16-bit integers. So you can
use mrc2tif in the same way as for K2.
However, because of the convolution algorithm, the compression ratio is
not as high as K2. Usually I get about 60 % of the original size.
If we had access to 'centroid-ed' super-resolution images before
convolution, we could save huge amount of storage...

For images from Falcon II, I don't know any good tricks.

Best regards,

Takanori Nakane

On 2018/06/03 10:17, Joshua Lobo wrote:
> Hi Dr Halfon
> 
> Spider has  a cp to tiff , imod has mrc2tiff . I haven't tried them but I
> think it's what you are looking for
> 
> Sincerely
> Joshua Lobo
> 
> On Sun, Jun 3, 2018, 10:02 AM Yehuda Halfon <[log in to unmask]>
> 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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