Export selected particles for publication


I would like to export high resolution images of the selected particles in addition to the selected 2D classes. Modifying the cryosparc-tools guidelines for exporting high resolution 2D classes, I was able to generate the attached image using the particles_selected/blob output and using the lowpass2 function in cryosparc-tools. However, the images don’t look nearly as good as the lowpass filtered images shown in the thumbnail of the selected 2D classes or for the extracted micrographs job. Is there a built-in function to lowpass filter and invert the particle micrographs to generate images similar to those shown in CryoSPARC?


lowpass2 should be the right function for lowpass filtering, and inverting can be done by just negating the pixel values of the images. Note that lowpass filtering for the thumbnails were controlled by a radwn parameter default to a value of 4, while in lowpass2 radwn is calculated from the input parameters arr, psize_A, and cutoff_resolution_A, using the equation radwn = (psize_A * arr.shape[-1]) / cutoff_resolution_A. So if you are using lowpass2 you would have to calculated the cutoff_resolution_A value for your images that would make radwn = 4