CsMT is a minimal CryoSPARC-workflow for cryo-EM reconstruction of decorated and undecorated microtubules developed by the Bui Lab & Cianfrocco Lab. Microtubules present unique challenges for single-particle analysis — including their inherent pseudo-helical symmetry, seam localisation, and decorated states. CsMT workflow uses a protofilament-based classification approach to solve MT structures.
- csMT_13pf_v1.0.9: Add Volume Tools for mask creation for Local Refinement after Symmetry Expansion
- csmt_13pf_1pf_v1_0_9_single_pf_refinement_branch: Branch for 1-PF refinement
- csMT_13pf_v1.0.8: First version of undecorated 13-PF analysis
The required software dependencies for this workflow are:
| Software | Tested Version | Purpose |
|---|---|---|
| CryoSPARC | v5.0.6 |
Primary processing framework |
| UCSF ChimeraX | v1.7 |
Ref/mask generation & map inspection |
For the full detailed explanation of Workflows features, refer to the CryoSPARC Workflow Guide.
-
Clone the Repository:
git clone https://github.com/builab/CsMT.git
-
Import Workflow into CryoSPARC:
- In your CryoSPARC instance, navigate to the Workflows sidebar panel.
- Click Import to load the pre-configured workflow JSON from CsMT.
- The
csmt_13pf_v1.X.Xworkflow will now appear in your Workflow panel. - For your microtubule reconstruction project, create a Project and a Workspace.
- Inside that Workspace, select the workflow and click Apply to run the CsMT workflow.
- The workflow
If you have any questions regarding the workflow, please put in the Issues in Github.
- CsMT Guideline
- YouTube Tutorial of Making References (To come)
- YouTube tutorial of Making Masks (To come)
If you use our workflow, please cite:
Tina Alagha, Asuva Arin, Nicolas Vangos, Helena Goodey-Parfitt, Hai Nguyen Ngo, Nhat Nam, Dau, Minh Hoa Nguyen, Thibault Legal, Michael Cianfrocco, Khanh Huy Bui. (2026). CsMT: a robust and streamlined CryoSPARC workflow for cryo-EM reconstruction of microtubules. bioRxiv 2026.07.31.741890; doi: https://doi.org/10.64898/2026.07.31.741890