> For the complete documentation index, see [llms.txt](https://guide.cryosparc.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://guide.cryosparc.com/processing-data.md).

# Processing Data in cryoSPARC

- [Get Started with CryoSPARC: Introductory Tutorial (v4.0+)](https://guide.cryosparc.com/processing-data/get-started-with-cryosparc-introductory-tutorial.md): In this tutorial, we will process a small dataset from movies to reconstructed density map. If you are new to data processing in CryoSPARC, we highly recommend following along!
- [Tutorial Videos](https://guide.cryosparc.com/processing-data/tutorial-videos.md): CryoSPARC tutorial videos.
- [All Job Types in CryoSPARC](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc.md): Details on all of the available job types in CryoSPARC, when to use them, required inputs, parameter explanations, and common next steps.
- [Import](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/import.md): Options for bringing data into CryoSPARC for processing.
- [Job: Import Movies](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/import/job-import-movies.md)
- [Job: Import Micrographs](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/import/job-import-micrographs.md)
- [Job: Import Particle Stack](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/import/job-import-particle-stack.md)
- [Job: Import 3D Volumes](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/import/job-import-3d-volumes.md)
- [Job: Import Templates](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/import/job-import-templates.md)
- [Job: Import Result Group](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/import/job-import-result-group.md)
- [Job: Import Beam Shift](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/import/job-import-beam-shift.md)
- [Motion Correction](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/motion-correction.md)
- [Job: Patch Motion Correction](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/motion-correction/job-patch-motion-correction.md)
- [Job: Full-Frame Motion Correction](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/motion-correction/job-full-frame-motion-correction.md)
- [Job: Local Motion Correction](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/motion-correction/job-local-motion-correction.md): Local motion correction.
- [Job: MotionCor2 (Wrapper) (BETA)](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/motion-correction/job-motioncor2-wrapper-beta.md): How to use the wrapper for MotionCor2 available in CryoSPARC.
- [Job: Reference Based Motion Correction (BETA)](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/motion-correction/job-reference-based-motion-correction-beta.md)
- [CTF Estimation](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/ctf-estimation.md)
- [Job: Patch CTF Estimation](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/ctf-estimation/job-patch-ctf-estimation.md): Patch-based CTF estimation.
- [Job: Patch CTF Extraction](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/ctf-estimation/job-patch-ctf-extraction.md): Patch CTF extraction.
- [Job: CTFFIND4 (Wrapper)](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/ctf-estimation/job-ctffind4-wrapper.md)
- [Job: Gctf (Wrapper) (Legacy)](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/ctf-estimation/job-gctf-wrapper-legacy.md)
- [Exposure Curation](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/exposure-curation.md): Curate micrographs (exposures) to remove low-quality data.
- [Job: Micrograph Denoiser (BETA)](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/exposure-curation/job-micrograph-denoiser-beta.md)
- [Job: Micrograph Junk Detector (BETA)](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/exposure-curation/job-micrograph-junk-detector-beta.md)
- [Interactive Job: Manually Curate Exposures](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/exposure-curation/interactive-job-manually-curate-exposures.md): Inspect, curate and reject exposures to remove low quality data.
- [Particle Picking](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/particle-picking.md): Identifying and selecting individual particles.
- [Interactive Job: Manual Picker](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/particle-picking/interactive-job-manual-picker.md): Manual picking.
- [Job: Blob Picker](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/particle-picking/job-blob-picker.md): Blob-based picking.
- [Job: Template Picker](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/particle-picking/job-template-picker.md): Template-based picking.
- [Job: Filament Tracer](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/particle-picking/job-filament-tracer-beta.md): Particle picking for filaments.
- [Job: Blob Picker Tuner](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/particle-picking/job-blob-picker-tuner.md): Optimize blob picker parameters.
- [Interactive Job: Inspect Particle Picks](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/particle-picking/interactive-job-inspect-particle-picks.md): Inspect and adjust particle picks.
- [Job: Create Templates](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/particle-picking/job-create-templates.md): Create templates for particle picking.
- [Extraction](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/extraction.md): Extracting picked particles from micrographs and related utilities.
- [Job: Extract from Micrographs](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/extraction/job-extract-from-micrographs.md): Extract picked particles from micrographs using a specified box size.
- [Job: Downsample Particles](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/extraction/job-downsample-particles.md): Downsample particles to save space.
- [Job: Restack Particles](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/extraction/job-restack-particles.md): Restack particles to manage your particle files and speed up caching
- [Deep Picking](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/deep-picking.md): Overview of deep particle picking methods available through CryoSPARC.
- [Guideline for Supervised Particle Picking using Deep Learning Models](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/deep-picking/guideline-for-supervised-particle-picking-using-deep-learning-models.md): Supervised particle picking.
- [Topaz (Bepler, et al)](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/deep-picking/topaz.md): Overview of the Topaz wrapper available through CryoSPARC.
- [T20S Proteasome: Topaz Particle Picking Tutorial](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/deep-picking/topaz/topaz-tutorial.md): Topaz particle picking tutorial via the Topaz wrapper available in CryoSPARC.
- [T20S Proteasome: Topaz Micrograph Denoising Tutorial](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/deep-picking/topaz/t20s-proteasome-deep-micrograph-denoising-tutorial.md): Topaz denoising tutorial via the Topaz wrapper available in CryoSPARC.
- [Job: Topaz Train and Job: Topaz Cross Validation](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/deep-picking/topaz/job-topaz-train-beta.md): Topaz job types available via wrapper in CryoSPARC.
- [Job: Topaz Extract](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/deep-picking/topaz/job-topaz-extract-beta.md): Topaz Extract job available via wrapper in CryoSPARC.
- [Job: Topaz Denoise](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/deep-picking/topaz/job-topaz-denoise-beta.md): Topaz Denoise job available via wrapper in CryoSPARC.
- [Deep Network Particle Picker (≤v4.7)](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/deep-picking/deep-network-particle-picker.md): Overview of the deep particle picker available through CryoSPARC.
- [T20S Proteasome: Deep Particle Picking Tutorial (≤v4.7)](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/deep-picking/deep-network-particle-picker/t20s-proteasome-deep-particle-picking-tutorial.md): Deep particle picking tutorial.
- [Job: Deep Picker Train and Job: Deep Picker Inference (≤v4.7)](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/deep-picking/deep-network-particle-picker/job-deep-picker-train-beta-and-deep-picker-extract-beta.md): Deep picking job types.
- [Particle Curation](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/particle-curation.md): 2D classification and curation of particles following particle picking.
- [Job: 2D Classification](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/particle-curation/job-2d-classification.md)
- [Interactive Job: Select 2D Classes](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/particle-curation/interactive-job-select-2d-classes.md)
- [Job: Reference Based Auto Select 2D (BETA)](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/particle-curation/job-reference-based-auto-select-2d-beta.md)
- [Job: Reconstruct 2D Classes](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/particle-curation/job-reconstruct-2d-classes.md)
- [Job: Rebalance 2D Classes](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/particle-curation/job-rebalance-2d-classes-beta.md)
- [Job: Class Probability Filter (Legacy)](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/particle-curation/job-class-probability-filter.md): Select a subset of extracted particles.
- [Job: Rebalance Orientations](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/particle-curation/job-rebalance-orientations.md)
- [Job: Subset Particles by Statistic](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/particle-curation/job-subset-particles-by-statistic.md)
- [3D Reconstruction](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/3d-reconstruction.md): Reconstruction of 3D volumes.
- [Job: Ab-Initio Reconstruction](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/3d-reconstruction/job-ab-initio-reconstruction.md): Ab-Initio reconstruction.
- [Job: Homogeneous Ab-Initio Refinement (BETA)](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/3d-reconstruction/job-homogeneous-ab-initio-refinement-beta.md)
- [3D Refinement](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/3d-refinement.md)
- [Job: Homogeneous Refinement](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/3d-refinement/job-homogeneous-refinement.md): Homogeneous refinement.
- [Job: Heterogeneous Refinement](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/3d-refinement/job-heterogeneous-refinement.md): Heterogeneous refinement.
- [Job: Non-Uniform Refinement](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/3d-refinement/job-non-uniform-refinement-new.md): Non-uniform refinement.
- [Job: Homogeneous Reconstruction Only](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/3d-refinement/job-homogeneous-reconstruction-only.md)
- [Job: Heterogeneous Reconstruction Only](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/3d-refinement/job-heterogeneous-reconstruction-only.md)
- [Job: Homogeneous Refinement (Legacy)](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/3d-refinement/job-homogeneous-refinement-legacy.md): Homogeneous refinement (Legacy).
- [Job: Non-uniform Refinement (Legacy)](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/3d-refinement/job-non-uniform-refinement-legacy.md): Non-uniform refinement (Legacy).
- [CTF Refinement](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/ctf-refinement.md): CTF refinement jobs and tutorials.
- [Job: Global CTF Refinement](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/ctf-refinement/job-global-ctf-refinement.md): Per-group beam tilt, trefoil, spherical aberration, tetrafoil.
- [Job: Local CTF Refinement](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/ctf-refinement/job-local-ctf-refinement.md): Per-particle defocus.
- [Job: Exposure Group Utilities](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/ctf-refinement/job-exposure-group-utilities.md): Exposure group utilities for combining or splitting exposure or particle datasets.
- [Conformational Variability](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/variability.md): Exploring conformational variability.
- [Job: 3D Variability](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/variability/job-3d-variability.md): 3DVA
- [Job: 3D Variability Display](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/variability/job-3d-variability-display.md): 3D variability display.
- [Job: 3D Classification](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/variability/job-3d-classification-beta.md): 3D classification without alignment.
- [Job: Regroup 3D Classes](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/variability/job-regroup-3d-classes.md): Regroup 3D classes via spectral clustering
- [Job: Reference Based Auto Select 3D (BETA)](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/variability/job-reference-based-auto-select-3d-beta.md)
- [Job: 3D Flexible Refinement (3DFlex) (BETA)](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/variability/job-3d-flexible-refinement-3dflex-beta.md)
- [Postprocessing](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/post-processing.md): Postprocessing jobs in CryoSPARC.
- [Job: Sharpening Tools](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/post-processing/job-sharpening-tools.md): Re-sharpen and adjust the B-factor of a volume after refinement.
- [Job: DeepEMhancer (Wrapper)](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/post-processing/job-deepemhancer-wrapper.md): Overview of the DeepEMhancer Wrapper in CryoSPARC.
- [Job: Validation (FSC)](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/post-processing/job-validation-fsc.md): FSC calculation.
- [Job: Local Resolution Estimation](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/post-processing/job-local-resolution-estimation.md): Local resolution estimation.
- [Job: Local Filtering](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/post-processing/job-local-filtering.md): Locally filter a refined map.
- [Job: ResLog Analysis](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/post-processing/job-reslog-analysis.md): ResLog analysis.
- [Job: ThreeDFSC (Wrapper) (Legacy)](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/post-processing/job-threedfsc-wrapper-legacy.md): Overview of the ThreeDFSC Wrapper in CryoSPARC.
- [Local Refinement](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/local-refinement.md): Local refinement and particle subtraction.
- [Job: Local Refinement](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/local-refinement/job-new-local-refinement-beta.md): Local refinement.
- [Job: Particle Subtraction](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/local-refinement/job-particle-subtraction-beta.md): Particle subtraction (signal subtraction).
- [Job: Local Refinement (Legacy)](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/local-refinement/job-local-refinement-beta.md): Local refinement (Legacy).
- [Helical Reconstruction](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/helical-reconstruction-beta.md): Helical processing.
- [Helical symmetry in CryoSPARC](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/helical-reconstruction-beta/helical-symmetry-in-cryosparc.md): Explanation of treatment of helical symmetry in CryoSPARC.
- [Job: Helical Refinement](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/helical-reconstruction-beta/job-helical-refinement-beta.md): Helical refinement.
- [Job: Symmetry search utility](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/helical-reconstruction-beta/job-symmetry-search-utility-beta.md): Symmetry search utility.
- [Job: Average Power Spectra](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/helical-reconstruction-beta/job-average-power-spectra.md)
- [Utilities](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/utilities.md): Utility jobs in CryoSPARC.
- [Job: Exposure Sets Tool](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/utilities/job-exposure-sets-tool.md): Split an exposure group into subsets or compare two groups.
- [Job: Exposure Tools](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/utilities/job-exposure-tools.md): Modify negative stain and phase plate values.
- [Job: Generate Micrograph Thumbnails](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/utilities/job-generate-micrograph-thumbnails.md): Generate preview thumbnails of micrographs.
- [Job: Cache Particles on SSD](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/utilities/job-cache-particles-on-ssd.md): Cache particles on a worker node so they're ready to be used as soon as resources are available.
- [Job: Check for Corrupt Particles](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/utilities/job-check-for-corrupt-particles.md): Check each particle stack .mrc file for corruption, including checking the header for length mismatch, NaN values check, and checksum verification.
- [Job: Particle Sets Tool](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/utilities/job-particle-sets-tool.md): Split a particle group into subsets or compare two groups.
- [Job: Reassign Particles to Micrographs](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/utilities/job-reassign-particles-to-micrographs.md): Link particles back to the micrographs they came from.
- [Job: Remove Duplicate Particles](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/utilities/job-remove-duplicate-particles.md): Remove duplicate particles.
- [Job: Symmetry Expansion](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/utilities/job-symmetry-expansion.md): Symmetry expansion.
- [Job: Volume Tools](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/utilities/job-volume-tools.md): Apply various operations including upsample, downsample, crop, pad, flip, etc., to a volume or mask.
- [Job: Volume Alignment Tools](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/utilities/job-volume-alignment-tools.md): Volume alignment tools.
- [Job: Align 3D maps](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/utilities/job-align-3d-maps.md): Align two or more 3D maps.
- [Job: Select Volume](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/utilities/job-select-volume.md): Select a volume and corresponding particle stack based on resolution.
- [Job: Split Volumes Group](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/utilities/job-split-volumes-group.md)
- [Job: Orientation Diagnostics](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/utilities/job-orientation-diagnostics.md): A new job in CryoSPARC v4.4+ to diagnose the presence of preferred orientation
- [Simulations](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/simulations.md): Simulation jobs.
- [Job: Simulate Data (GPU)](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/simulations/job-simulate-data-gpu.md): Generate simulated particles from an input volume.
- [Job: Simulate Data (Legacy)](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/simulations/job-simulate-data-legacy.md): Generate simulated particles.
- [Automated Workflows](https://guide.cryosparc.com/processing-data/automated-workflows.md): Get started with automated, end-to-end data processing in CryoSPARC.
- [Advanced automated data processing: a case study using CAK](https://guide.cryosparc.com/processing-data/automated-workflows/advanced-automated-data-processing-a-case-study-using-cak.md)
- [Full automated data processing: a case study using GPCRs](https://guide.cryosparc.com/processing-data/automated-workflows/full-automated-data-processing-a-case-study-using-gpcrs.md)
- [Practical tips: using Workflows to process your own data](https://guide.cryosparc.com/processing-data/automated-workflows/practical-tips-using-workflows-to-process-your-own-data.md)
- [Downloads: Workflow JSONs, sample volumes, and masks](https://guide.cryosparc.com/processing-data/automated-workflows/downloads-workflow-jsons-sample-volumes-and-masks.md): Dedicated space for all downloads related to automated workflows for CryoSPARC
- [CryoSPARC Tools](https://guide.cryosparc.com/processing-data/cryosparc-tools.md)
- [Data Processing Tutorials](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies.md): Tutorials on how to use CryoSPARC jobs and processing cryo-EM data.
- [Case Study: Discrete heterogeneity in a sample of Acetogenin-bound complex I (EMPIAR 10927)](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/case-study-discrete-heterogeneity-in-a-sample-of-acetogenin-bound-complex-i-empiar-10927.md): Processing EMPIAR-10927 including separating targets using Per-particle scales or custom settings in Ab-Initio Reconstruction, and using 3DVA to guide sub-classification choices.
- [Case Study: processing of a novel motor-bound nucleosome state (EMPIAR-10739) - part 2](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/case-study-processing-of-a-novel-motor-bound-nucleosome-state-empiar-10739-part-2.md): Processing EMPIAR-10739 including using 3DVA to guide classification strategies, separating low population classes, and local refinement of a flexible region.
- [Case Study: End-to-end and exploratory processing of a motor-bound nucleosome (EMPIAR-10739)](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/case-study-end-to-end-and-exploratory-processing-of-a-motor-bound-nucleosome-empiar-10739.md): Processing EMPIAR-10739 including handling global pseudosymmetry, using 3DVA to guide classification strategies, separating low population classes, and local refinement of a flexible region.
- [Case study: End-to-end processing of a ligand-bound GPCR (EMPIAR-10853)](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/case-study-end-to-end-processing-of-a-ligand-bound-gpcr-empiar-10853.md): Processing EMPIAR-10853 including Micrograph Denoising, Micrograph Junk Detector, Subset Particles by Statistic, Local Refinement and focussed 3D Classification to improve ligand density.
- [Case Study: DkTx-bound TRPV1 (EMPIAR-10059)](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/case-study-dktx-bound-trpv1-empiar-10059.md): Processing EMPIAR-10059 in CryoSPARC v4.6 with a focus on particle curation, developing an intuition for when a domain may be blurred due to flexibility, and how to handle this type of flexibility.
- [Case Study: Pseudosymmetry in TRPV5 and Calmodulin (EMPIAR-10256)](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/case-study-pseudosymmetry-in-trpv5-and-calmodulin-empiar-10256.md): Processing EMPIAR-10256 with a focus on handling pseudosymmetry and 3D Classification parameter choices.
- [Case Study: End-to-end processing of an inactive GPCR (EMPIAR-10668)](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/case-study-end-to-end-processing-of-an-inactive-gpcr-empiar-10668.md): Processing EMPIAR-10668 including Local Refinement, 3D Variability Analysis, 3D Flex and classification of continuous heterogeneity.
- [Case Study: End-to-end processing of encapsulated ferritin (EMPIAR-10716)](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/case-study-end-to-end-processing-of-encapsulated-ferritin-empiar-10716.md): Processing EMPIAR-10716 with a focus on high-symmetry ab-initio reconstruction, local symmetry, non-point-group symmetry, symmetry expansion, and custom geometry operations.
- [Case Study: Discrete and Continuous Heterogeneity in FaNaC1 (EMPIAR-11631 and -11632)](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/case-study-discrete-and-continuous-heterogeneity-in-fanac1-empiar-11631-and-11632.md): Processing a combined dataset of an ion channel with a focus on techniques for separating conformational states from a heterogeneous mixture.
- [Case Study: Picking-induced Orientation Bias in HA Trimer (EMPIAR-10096 and -10097)](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/case-study-picking-induced-orientation-bias-in-ha-trimer-empiar-10096-and-10097.md): An analysis of the impact of data collection and particle picking techniques on orientation bias, including strategies for improving map quality and isotropy.
- [Case Study: Exploratory data processing by Oliver Clarke](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/case-study-exploratory-data-processing-by-oliver-clarke.md)
- [Case Study: Processing EMPIAR-10291 (300 Micrographs) to 3.4Å in 1 hour 25 minutes](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/case-study-processing-empiar-10291-300-micrographs-to-3.4a-in-1-hour-25-minutes.md): Processing EMPIAR-10291 from micrographs to a 3D reconstruction.
- [Tutorial: Tips for Membrane Protein Structures](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/tutorial-tips-for-membrane-protein-structures.md): Helpful hints for processing cryo-EM data of membrane proteins.
- [Tutorial: Common CryoSPARC Plots](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/tutorial-common-cryosparc-plots.md): A detailed description of the common plots that CryoSPARC makes across multiple job types.
- [Tutorial: Negative Stain Data](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/negative-stain-data.md): Learn how to work with negative stain data in CryoSPARC.
- [Tutorial: Phase Plate Data](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/phase-plate-data.md): Learn how to work with Phase Plate data in CryoSPARC.
- [Tutorial: EER File Support](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/tutorial-eer-file-support.md): Learn how to work with EER files in CryoSPARC.
- [Tutorial: EPU AFIS Beam Shift Import](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/tutorial-epu-afis-beam-shift-import.md): A tutorial covering how to split exposures into groups based on beam shift values, for data collected in EPU's AFIS mode.
- [Tutorial: Patch Motion and Patch CTF](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/tutorial-patch-motion-and-patch-ctf.md): This tutorial covers Patch Motion Correction and Patch CTF Estimation.
- [Tutorial: Float16 Support](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/tutorial-float16-support.md)
- [Tutorial: Particle Picking Calibration](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/tutorial-particle-picking-calibration.md): In cryoSPARC v2.13+, there is a new feature that directly calibrates pick scores against defocus, making it much easier to set thresholds when using the Inspect Picks job.
- [Tutorial: Blob Picker Tuner](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/tutorial-blob-picker-tuner.md): Optimize blob picks with the Blob Picker Tuner.
- [Tutorial: Helical Processing using EMPIAR-10031 (MAVS)](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/case-study-empiar-10031-mavs.md): Case study on using helical processing tools.
- [Tutorial: Maximum Box Sizes for Refinement](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/performance-metrics.md): Maximum box sizes for various amounts of GPU memory (VRAM).
- [Tutorial: CTF Refinement](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/tutorial-ctf-refinement.md): This tutorial details the background, implementation, and use of CTF refinement in CryoSPARC v2.12+.
- [Tutorial: Ewald Sphere Correction](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/tutorial-ewald-sphere-correction.md): How to work with Ewald Sphere Correction.
- [Tutorial: Symmetry Relaxation](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/tutorial-symmetry-relaxation.md): A tutorial detailing symmetry relaxation in CryoSPARC, a tool to help improve the refinement of pseudosymmetric particles.
- [Tutorial: Orientation Diagnostics](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/tutorial-orientation-diagnostics.md): Using the new Orientation Diagnostics job to assess preferred orientation with titled and untilted HA Trimer data
- [Tutorial: BILD files](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/tutorial-bild-files.md): An overview of BILD files in CryoSPARC
- [Tutorial: Mask Creation](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/mask-selection-and-generation-in-ucsf-chimera.md): Mask Selection and Generation in UCSF ChimeraX
- [Tutorial: Dynamic Masking in Refinements (v5.0+)](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/tutorial-dynamic-masking-in-refinements-v5.0.md)
- [Case Study: Yeast U4/U6.U5 tri-snRNP](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/case-study-yeast-u4-u6.u5-tri-snrnp.md): Processing EMPIAR-10073 with a focus on Local Refinement.
- [Tutorial: 3D Classification](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/tutorial-3d-classification.md): 3D Classification is a new way to perform discrete heterogeneity analysis in CryoSPARC in a manner that complements Heterogeneous Refinement.
- [Tutorial: 3D Variability Analysis (Part One)](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/tutorial-3d-variability-analysis-part-one.md): Part One of the two-part tutorial on 3D Variability Analysis for exploring heterogeneity.
- [Tutorial: 3D Variability Analysis (Part Two)](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/tutorial-3d-variability-analysis-part-two.md): Part Two of the two-part tutorial on 3D Variability Analysis for exploring heterogeneity.
- [Tutorial: 3D Flexible Refinement](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/tutorial-3d-flexible-refinement.md): An in-depth guide to 3D Flexible Refinement (3DFlex) in CryoSPARC.
- [Installing 3DFlex Dependencies (v4.1–v4.3)](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/tutorial-3d-flexible-refinement/installing-3dflex-dependencies.md)
- [Tutorial: 3D Flex Mesh Preparation](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/tutorial-3d-flex-mesh-preparation.md)
- [Webinar Recordings](https://guide.cryosparc.com/processing-data/webinar-recordings.md): CryoSPARC webinar recordings.