We offer single particle cryo-EM software for analyzing stacks of extracted particles. At the moment, we do not offer end-to-end single particle analysis (motion correction through to final 3D refinements).
Currently available tools
- RELION-v3.1
- 2D classification – 2D averaging & classification
- 3D classification – 3D averaging & classification
- 3D refinement – iteratively refine particle orientations to achieve the highest resolution
- Multibody refinement – separately refine and reconstruct sub-regions in a 3D reconstruction
- SPHIRE
- ISAC (iterative stable alignment & classification): performs 2D classification on particle stacks to recover rare states
- cryoDRGN – deep learning-based analysis of protein conformational landscapes
- DeepEMhancer – map modification to sharpen 3D reconstructions
- Local map interrogation/modification
- LocSpiral – Sharpen map using spiral phase transform
- LocBfactor – Estimate and sharpen maps with local B-factors
- LocOccupancy – estimate occupancy of a region in 3D reconstruction
- Conversion software
- csparc2star – convert cryoSPARC .cs file to .star format for RELION
- Efficiency – measure the distribution of particle orientations in a 3D reconstruction
- Align Projections – align reprojections of 3D reconstruction with 2D class averages
Tools organized by job purpose
- 2D classification
- RELION, ISAC
- 3D classification
- RELION
- 3D refinement for high-resolution
- RELION
- 3D flexibility analysis
- RELION Multibody, cryoDRGN
- Map modification
- DeepEMhancer, LocSpiral, LocBfactor, LocOccupancy
- Validation
- Efficiency, Align Projections
- Conversion
- csparc2star
Questions? Email cosmic2support@umich.edu