Change the pixel size of the imported volume

Features and Functionality
1

Dear colleagues,

Is there an option to change the pixel size of the imported volume?

Thank you

Sincerely,
Dmitry

2

Hi Dmitry,

In the import volume job, there is a ā€˜pixel size (A)ā€™ parameter, where you can specify desired pixel size.

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3

Hello,

Also in Volume Tools

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4

Thank you, @joonpark - but what I want to do is to resize the volume when it is already loaded. Any tips for that?

5

Iā€™m not aware of tools in cryoSPARC that can change pixel size after finishing importing. Iā€™m not sure what you are trying to do, but you can simply re-run the import job. Or you can import the same volume again in a different import job with new pixel size.

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6

thank you @carlos - I got a little confused with the usage of it. What I need is to resize the pixel size after the import. Is that possible?

7

Wellā€¦ it looks like, although I never tried: https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/utilities/job-volume-tools
The guide is pretty useful, some of the descriptions are very short, but still useful.

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8

Thank you, Carlos. Indeed the descriptions are helpful. I find the absence of the visual examples a little confusing since the listed parameters do not correspond to the ones from the software.

E.g.

image
image308Ɨ1318 34.8 KB

9

Hehe thatā€™s trueā€¦ but I prefer them to keep working on improving the software and leaving the doc a bit as second priority. That said, the doc is always improving as well - itā€™s the best I know among all the CryoEM programs, with their tutorials and more - , plus we have this discussion page that helps us making contact.

I hope you found the option you were looking for?

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10

@Dmitry Given the confusing naming of operations, can you please specify which of ā€œcropā€ (reduce padding/remove outer edges of the volume) or ā€œresampleā€ (change the resolution and box size, but maintain the extent of padding and volume) better describes your needs? If itā€™s neither of the options, knowing more about your use case and reason, such as computational time or memory constraints, for adjusting the pixel representation of the volume may help us propose a strategy.

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11

Dear Carlos,

Yes, I finally did that with different combinations // programs and many peopleā€™s expertise.

Thank you for your input!

Kind regards,
Dmitry