[3dem] Data storage and compression

[Carlos Oscar S. Sorzano]

Dear all,

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.

Kind regards, Carlos Oscar

El 29/08/2019 a las 21:35, Ali Punjani escribió:
> Hi Matthew,
>
> 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.
>
> Ali
>
> On Thu, Aug 29, 2019 at 3:19 PM Matthew H. Cahn <mcahn at princeton.edu 
> <mailto:mcahn at princeton.edu>> wrote:
>
>     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?
>
>     — Matthew
>
>     *||  Matthew Cahn  |  Linux Administrator  |  Dept. of Molecular
>     Biology / Research Computing  |  Princeton University  |  (609)
>     258-5404  | mcahn at princeton.edu <mailto:mcahn at princeton.edu>  ||
>     *
>
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-- 
------------------------------------------------------------------------
Carlos Oscar Sánchez Sorzano                  e-mail:   coss at cnb.csic.es
Biocomputing unit                             http://i2pc.es/coss
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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