How to get low pass filtered result

[qhz991029]

Hello!

When importing particle stack, it will show raw images and low pass filtered images. I wonder how could I perform low pass filtering to get the similar result to the filtered one?

[wtempel]

@qhz991029 Please can you provide more details on the source, format and dimensions of the inputs as well as the desired format and intended use of the filtered outputs.

[qhz991029]

Thank you so much for your reply!

The input is just a particle stack, namely a .star file. I am trying to low pass filter particle images for other downstream tasks but cannot find this function in CryoSPARC. The result from CryoSPARC is much better than my trial, which simply cut off high frequency in Fourier domain. I wonder if I can get these low pass filtered images through some functions.

[CryoEM2]

also called “thumbnail” of particle image (should be several searchable topics using that name). long requested, and at some point implemented with cryosparc tools. Nothing in the GUI as far as I know.

Thumbnails of particle stacks?

Hi @dmsmith and @CryoEM1 , Thanks for the post! In CryoSPARC v4.1 (released December 12, 2022), we’re excited to announce a new Python library, cryosparc-tools, that allows you perform tasks like this much easier: Getting Started — cryosparc-tools We have an example of how to generate high-resolution 2D class images. Producing images of particle stacks should be similar. - Suhail

[kstachowski]

Hi @qhz991029,

For items used in downstream processing, we recommend taking advantage of the downsampling job, limiting particle/volume alignment resolutions, and lowpass filtering resulting volumes, and recommend against modifying the information content of particles stacks in this context as this could get messy.

If you intend to use these particle for visualization purposes, @rposert has provided a good script that allows you to do this using CS-tools.

All the best,
Kye