Category Topics

3D Refinement

Questions, discussion and errors relating to homogeneous and heterogeneous (multi-reference) refinement, and non-uniform refinement.
323

Import and Export

Questions, discussion and errors encountered when importing and exporting movies, micrographs, particles, volumes and other files.
424

Particle Picking

Questions, discussion and error messages relating to particle picking (manual, blob-based, template-based, deep picking), particle extraction and inspection.
259

Cryo-EM Data Processing

General questions and discussion relating to cryo-EM image processing and methods.
110

Troubleshooting

Report and troubleshoot errors encountered when processing data. Please be as specific as possible and follow the Troubleshooting Guidelines.
1371

Install, Configure and Update

How to install, configure and update cryoSPARC on a workstation or cluster. Please refer to these instructions first.
952

3D Flexible Refinement

Questions and Discussion regarding 3DFlex jobs (Data Prep, Mesh Prep, Training, Generator, Reconstruction)
91

Local Refinement

Questions, discussion and errors encountered when using local refinement and signal subtraction.
126
42

Utilities

For discussion about Volume Tools, Sharpening Tools, Particle Sets Tools, Exposure Sets Tools, etc.
74

Exposure Curation

Questions, discussion and error messages arising when curating and inspecting micrographs.
39

Motion Correction

Questions, discussion and errors encountered when performing patch-based, global and local motion correction.
254

CTF Estimation

Questions, discussion and errors encountered when estimating CTF values.
61

Application

Topics related to the CryoSPARC web application/user interface.
156

CryoSPARC Live

Questions, issues and feature requests relating to cryoSPARC Live.
147

Features and Functionality

Requests for new jobs and features in cryoSPARC. If you have questions about an existing job or feature, please submit them under the appropriate category (e.g., 3D reconstruction, CryoSPARC Parameters, etc.).
539

CTF Refinement

Questions and issues related to CTF refinement (global and per-particle).
42

3D Reconstruction

Questions, discussion and errors encountered when performing homogeneous and heterogeneous ab-initio reconstruction.
95

2D Classification

Questions, discussion and error messages relating to 2D classification of particles.
173

Data Management

Questions and discussion relating to data management for cryo-EM.
97

Cryo-EM Sample Preparation

Topics related to the preparation of samples for cryogenic electron microscopy.
8

Model Building

Questions and discussions around the building, refinement and validation of molecular models based on cryo-EM data.
9

Helical Processing

Questions relating to helical processing.
71

Tips

Best practices and how-tos for using and getting the most out of cryoSPARC.
145

3D Classification

Questions and discussion regarding 3D Classification.
74

Scripting

Scripting in or with CryoSPARC: CryoSPARC CLI, cryosparc-tools, etc.
33

3D Variability Analysis

Questions and discussion regarding the 3D variability analysis and 3D variability display.
120

CryoSPARC Parameters

Questions about job parameters and how to optimize these.
17

Post Processing

Questions, discussion and errors relating to post processing job types, including local resolution estimation, local filtering, align 3D maps, reslog type analysis, and 3DFSC analysis.
40

Data Processing Strategy

Questions and advice on data processing strategy for particular samples or datasets. Discussion and best practices/tips are welcome!
12

Hardware and Performance

Questions and discussion relating to hardware setup and cryoSPARC performance.
80