Question about filament tracer

Features and Functionality
1

Hi, I am trying the CryoSPARC filament tracer on microtubule doublet. Given the templates I provided and the appearance of the doublets, it is kind of understandable that CryoSPARC decides to draw three lines/traces for each microtubule doublet :joy: but I wonder if there is any parameters I can tweak to use only the middle trace.
templates

micrograph
micrograph936×673 158 KB

tracer
tracer735×623 113 KB

Thanks!
Rui

2

Hi! For filament tracer parameters I would increase filament diameter (max and min as well in template free) and/or the separation distance between segments. Just to see if the job can be forced to only place the middle trace. If this doesn’t work, I would use a large extraction box size in the next job to see if I can capture the whole doublet just from the middle trace. I think the 2D classes you shared look great but I do not know much about tubules haha.

3

Hi @zhangrui_wustl,

Thanks for the post :slight_smile: I second @TCEvans comments; you’ll likely need to increase the filament diameter for this, and 2D classification may be helpful in getting rid of edge picks. For a more detailed description of the parameters, check out our guide page on the job. The diagnostic plots can also help determine where the extra picks are getting picked up. Ultimately, it may be difficult for the filament tracer to separate the “center” picks from “side” picks, as the provided templates end up getting the algorithm to simply look for bright lines in the data.

Best,
Michael

4

Hi @mmclean and @TCEvans ,

Thank you so much for your reply!

Thanks!
Rui