I’m in the process of evaluating the new Reference based motion correction tool, and I have a couple of questions/suggestions:
For extraction, how is the box size is set? Is this inherited from the input particles? There’s an option to f-crop the output particles, but it would also be helpful to be able to specify a box size and maybe even further downsampling (eg 320 px → 160 px).
This is in the job documentation:
Output F-crop factor parameter can be used to reduce the size of the output particles by Fourier-space cropping. By default, the particles are extracted using the raw pixel size of the movies (including the upsampling factor, in the case of EER movies), and at whatever box size is necessary for the extracted particles to have the same physical extent as the reference volume. Note that this does not necessarily equate with the motion corrected pixel size used in earlier processing steps (e.g., super-resolution movies).
I haven’t tried re-scaling the input volume first, my instinct says it wouldn’t work.
ha, totally missed that - thanks!
@gdodge For now, if you prefer to specify your output downsampling target as a pixel count, rather than an F-crop ratio, you may subsequently run a Downsample Particles job.