3D Flex standard deviations

In the 3D flex pre-print, in several figures the authors display convected volumes at +1 and -1 standard deviations in the latent space. How would I do this for my own figures? Does the 3D flex generator job automatically output a volume series from +1 to -1 standard deviations? In that case I assume I just use the first and last frames for comparison.

Cheers! :slight_smile:

Hi @scottgardner,

In the 3D Flex generator job, the latents vary by default from the 2nd to the 98th percentile for each dimension. To instead run the generator but querying latent variables from -1 to +1 standard deviations, the best approach would be by using CryoSPARC Tools and following the " 3D Flex: Custom Latent Trajectory" example, which shows how this may be done for a more advanced custom trajectory. In your case, you wouldn’t need the interactive component to that notebook; it would be sufficient to calculate the standard deviation of the latent z values for each dimension, and then output a linearly spaced sampling in the same fashion as shown by the notebook.

The notebook shows how to output these custom latents to a CryoSPARC workspace as an External Job. These latents can then be passed into the flex generator job to actually create the volumes at each latent coordinate :slight_smile:

Hope this helps,

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Awesome, thanks a lot! :slight_smile: