[3dem] Data storage and compression

[Takanori Nakane]

Hi,

> Most people just opt for the "hard drive on a shelf" method for completed
> projects, which has advantages (cheap/simple) and disadvantages (what
> happens if the drive dies)...

After publication of your structures, I recommend raw data to be deposited
in EMPIAR.
Not only is it useful for reproducibility, education and method development,
it also serves as an additional layer of backup. You might drop your disk,
water might leak from the ceiling, etc. Having backups in a physically
distant
place is a good practice.

Best regards,

Takanori Nakanori

> Julien,
> are you referring to the raw data, or are you trying to archive all of the
> files associated with a project?
>
> Counting-mode movies are generally stored and archived as compressed tiff
> stacks, though if they are collected on a Falcon, there are issues with
> this, as good compression is achieved only pre-normalization (or
> post-normalization if you decide you are willing to switch back to an
> integer format).
>
> If you want to perfectly archive everything exactly as it is (losslessly),
> some compression algorithms may do very slightly better than others, but
> pretty much any of the commonly used algorithms will do about the same.
> Usually the slower ones will do slightly better, but you have to decide if
> it's worth the CPU time the compression takes.  By definition, the noisier
> the data is, the less compressible it is, unless you are willing to invoke
> "lossy" compression and throw away some of the bits of pure noise.
>
> Most people just opt for the "hard drive on a shelf" method for completed
> projects, which has advantages (cheap/simple) and disadvantages (what
> happens if the drive dies)...
>
> --------------------------------------------------------------------------------------
> Steven Ludtke, Ph.D. <sludtke at bcm.edu<mailto:sludtke at bcm.edu>>
>          Baylor College of Medicine
> Charles C. Bell Jr., Professor of Structural Biology
> Dept. of Biochemistry and Molecular Biology
> (www.bcm.edu/biochem<http://www.bcm.edu/biochem>)
> Academic Director, CryoEM Core
> (cryoem.bcm.edu<http://cryoem.bcm.edu>)
> Co-Director CIBR Center
> (www.bcm.edu/research/cibr<http://www.bcm.edu/research/cibr>)
>
>
>
> On Aug 29, 2019, at 6:30 AM, Julien Bous
> <julien.bous at etu.umontpellier.fr<mailto:julien.bous at etu.umontpellier.fr>>
> wrote:
>
>
>
> Dear Community,
>
> I have a question about the best way to store my data once SPA projects
> are achieved. Can you advise me about which compression format is to
> prefer?
>
> Thank you for your interest,
>
> Julien
>
>
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