# CryoSPARC Guide ## CryoSPARC Guide - [About CryoSPARC™](https://guide.cryosparc.com/readme.md): General information about the software platform. - [Licensing](https://guide.cryosparc.com/licensing.md): Non-profit and commercial licensing options. - [Non-commercial license agreement](https://guide.cryosparc.com/licensing/non-commercial-license-agreement.md): Full text of CryoSPARC non-commercial license agreement. Please send any queries to: info@structura.bio. - [CryoSPARC Architecture and System Requirements](https://guide.cryosparc.com/setup-configuration-and-management/hardware-and-system-requirements.md): Description of CryoSPARC HPC software system architecture, typical setups (e.g., workstation, cluster). - [CryoSPARC Installation Prerequisites](https://guide.cryosparc.com/setup-configuration-and-management/cryosparc-installation-prerequisites.md): Before installing CryoSPARC, ensure these six requirements are met. - [How to Download, Install and Configure](https://guide.cryosparc.com/setup-configuration-and-management/how-to-download-install-and-configure.md): Meeting system requirements, obtaining a License ID, and downloading & installing CryoSPARC. - [Obtaining A License ID](https://guide.cryosparc.com/setup-configuration-and-management/how-to-download-install-and-configure/obtaining-a-license-id.md): Fill out the form to obtain a License ID required for installing and using CryoSPARC. - [Downloading and Installing CryoSPARC](https://guide.cryosparc.com/setup-configuration-and-management/how-to-download-install-and-configure/downloading-and-installing-cryosparc.md): Downloading and installing the cryosparc\_master and cryosparc\_worker packages. - [CryoSPARC Cluster Integration Script Examples](https://guide.cryosparc.com/setup-configuration-and-management/how-to-download-install-and-configure/cryosparc-cluster-integration-script-examples.md): Examples of cluster\_info.json and cluster\_script.sh scripts for various cluster workload managers - [Accessing the CryoSPARC User Interface](https://guide.cryosparc.com/setup-configuration-and-management/how-to-download-install-and-configure/accessing-cryosparc.md): Viewing the user interface locally and from home - [(Optional) Hosting CryoSPARC Through a Reverse Proxy](https://guide.cryosparc.com/setup-configuration-and-management/how-to-download-install-and-configure/optional-hosting-cryosparc-through-a-reverse-proxy.md) - [Software Updates and Patches](https://guide.cryosparc.com/setup-configuration-and-management/software-updates.md): How to get the latest CryoSPARC features and fixes or roll back to a previous version. - [Management and Monitoring (≤v4.7)](https://guide.cryosparc.com/setup-configuration-and-management/management-and-monitoring-4.7.md): Instructions for accessing and working in the CryoSPARC command line. - [Environment variables (≤v4.7)](https://guide.cryosparc.com/setup-configuration-and-management/management-and-monitoring-4.7/environment-variables-v4.7.md): (Advanced) Specify additional environment variables in the configuration files to augment CryoSPARC's low-level behaviour. - [cryosparcm reference (≤v4.7)](https://guide.cryosparc.com/setup-configuration-and-management/management-and-monitoring-4.7/cryosparcm-4.7.md): How to use the cryosparcm utility for starting and stopping the CryoSPARC instance, checking status or logs, managing users and using CryoSPARC's command-line interface. - [cryosparcm cli reference (≤v4.7)](https://guide.cryosparc.com/setup-configuration-and-management/management-and-monitoring-4.7/cli-4.7.md): How to use CryoSPARC's low-level command-line interface. - [cryosparcw reference (≤v4.7)](https://guide.cryosparc.com/setup-configuration-and-management/management-and-monitoring-4.7/cryosparcw-4.7.md): How to use the cryosparcw utility for managing CryoSPARC workers - [Management and Monitoring (v5.0+)](https://guide.cryosparc.com/setup-configuration-and-management/management-and-monitoring-v5.0.md): Instructions for accessing and working in the CryoSPARC command line. - [Environment Variables (v5.0+)](https://guide.cryosparc.com/setup-configuration-and-management/management-and-monitoring-v5.0/environment-variables-v5.0.md): (Advanced) Specify additional environment variables in the configuration files to augment CryoSPARC's low-level behaviour. - [cryosparcm reference (v5.0+)](https://guide.cryosparc.com/setup-configuration-and-management/management-and-monitoring-v5.0/cryosparcm-reference-v5.0.md): How to use the cryosparcm utility for starting and stopping the CryoSPARC instance, checking status or logs, managing users and using CryoSPARC's command-line interface. - [cryosparcm cli reference (v5.0+)](https://guide.cryosparc.com/setup-configuration-and-management/management-and-monitoring-v5.0/cryosparcm-cli-reference-v5.0.md): How to use CryoSPARC's low-level command line interface to perform actions that can be performed in the UI. - [cryosparcw reference (v5.0+)](https://guide.cryosparc.com/setup-configuration-and-management/management-and-monitoring-v5.0/cryosparcw-reference-v5.0.md): How to use the cryosparcw utility for managing CryoSPARC workers - [Software System Guides](https://guide.cryosparc.com/setup-configuration-and-management/software-system-guides.md): CryoSPARC software management guides. - [Guide: Updating to CryoSPARC v5](https://guide.cryosparc.com/setup-configuration-and-management/software-system-guides/guide-updating-to-cryosparc-v5.md): CryoSPARC v5 is backwards compatible with v4. The update process includes new validation steps that may take some time, up to one hour for larger instances. - [Guide: Updating to CryoSPARC v4](https://guide.cryosparc.com/setup-configuration-and-management/software-system-guides/guide-updating-to-cryosparc-v4.md): Installing or updating to CryoSPARC v4 is similar to previous versions of CryoSPARC, but downgrading is not possible past v3.4.0. - [Guide: Installation Testing with cryosparcm test](https://guide.cryosparc.com/setup-configuration-and-management/software-system-guides/guide-installation-testing-with-cryosparcm-test.md): This guide covers how to use cryosparcm test to verify your CryoSPARC installation is working properly. - [Guide: Verify CryoSPARC Installation with the Extensive Validation Job (v4.3+)](https://guide.cryosparc.com/setup-configuration-and-management/software-system-guides/tutorial-verify-cryosparc-installation-with-the-extensive-workflow-sysadmin-guide.md) - [Guide: Verify CryoSPARC Installation with the Extensive Workflow (≤v4.2)](https://guide.cryosparc.com/setup-configuration-and-management/software-system-guides/tutorial-verify-cryosparc-installation-with-the-extensive-workflow-sysadmin-guide-1.md) - [Guide: Performance Benchmarking (v4.3+)](https://guide.cryosparc.com/setup-configuration-and-management/software-system-guides/guide-performance-benchmarking-v4.3.md): This guide covers the new benchmarking tool in CryoSPARC that allows for benchmarking a worker’s filesystem, CPUs and GPUs. Available in CryoSPARC v4.3.0+. - [Guide: Download Error Reports](https://guide.cryosparc.com/setup-configuration-and-management/software-system-guides/guide-download-error-reports.md): How to download job and system-level error reports from within the application. - [Guide: Maintenance Mode and Configurable User Facing Messages](https://guide.cryosparc.com/setup-configuration-and-management/software-system-guides/guide-maintenance-mode-and-configurable-user-facing-messages.md): Pause the job queue during updates and set optional user facing messages. - [Guide: User Management](https://guide.cryosparc.com/setup-configuration-and-management/software-system-guides/tutorial-user-management.md): User creation, management, setting roles and password management through the CryoSPARC user interface. - [Guide: Multi-user Unix Permissions and Data Access Control](https://guide.cryosparc.com/setup-configuration-and-management/software-system-guides/unix-permissions-and-data-access-control.md): Tips on how to manage permissions and data access control. - [Guide: Lane Assignments and Restrictions](https://guide.cryosparc.com/setup-configuration-and-management/software-system-guides/guide-lane-assignments-and-restrictions.md): Assigning CryoSPARC users to specific scheduler lanes. - [Guide: Priority Job Queuing](https://guide.cryosparc.com/setup-configuration-and-management/software-system-guides/tutorial-priority-job-queuing.md): How to prioritize jobs to override the CryoSPARC scheduler's default behaviour. - [Guide: Configuring Custom Variables for Cluster Job Submission Scripts](https://guide.cryosparc.com/setup-configuration-and-management/software-system-guides/guide-configuring-custom-variables-for-cluster-job-submission-scripts.md) - [Guide: SSD Particle Caching in CryoSPARC](https://guide.cryosparc.com/setup-configuration-and-management/software-system-guides/tutorial-ssd-particle-caching-in-cryosparc.md): Overview of how SSD particle caching works, how much SSD space you need, configuration options and troubleshooting. - [Guide: Data Management in CryoSPARC (v4.0+)](https://guide.cryosparc.com/setup-configuration-and-management/software-system-guides/guide-data-management-in-cryosparc-v4.0.md): An overview of all data management utilities and common use cases. - [Guide: Data Cleanup (v4.3+)](https://guide.cryosparc.com/setup-configuration-and-management/software-system-guides/guide-data-cleanup-v4.3.md): New features in v4.3+ for managing and cleaning up project data. - [Guide: Reduce Database Size (v4.3+)](https://guide.cryosparc.com/setup-configuration-and-management/software-system-guides/guide-reduce-database-size-v4.3.md): A guide on reducing the size of large CryoSPARC databases using methods provided by MongoDB. - [Guide: CryoSPARC Live Session Data Management (≤v4.7)](https://guide.cryosparc.com/setup-configuration-and-management/software-system-guides/cryosparc-live-session-data-management-4.7.md): How to manage the data created by your cryoSPARC Live Sessions via the user interface and data management API. - [Guide: Instance Recovery (v5.0+)](https://guide.cryosparc.com/setup-configuration-and-management/software-system-guides/guide-instance-recovery-v5.0.md): How to recover a CryoSPARC instance if the database directory is corrupted or lost. - [Guide: Migrating your CryoSPARC Instance](https://guide.cryosparc.com/setup-configuration-and-management/software-system-guides/tutorial-migrating-your-cryosparc-instance.md): A guide to moving CryoSPARC from one location to another. - [Deploying CryoSPARC on AWS](https://guide.cryosparc.com/setup-configuration-and-management/cryosparc-on-aws.md): Version 1.0 (May 10, 2021) - [Performance Benchmarks](https://guide.cryosparc.com/setup-configuration-and-management/cryosparc-on-aws/performance-benchmarks-aws.md): Version 1.0 (May 10, 2021) - [Troubleshooting](https://guide.cryosparc.com/setup-configuration-and-management/troubleshooting.md): Overview of common issues and advice on how to resolve them. - [A Tour of the CryoSPARC Interface](https://guide.cryosparc.com/application-guide/a-tour-of-the-cryosparc-interface.md) - [Browsing the CryoSPARC Instance](https://guide.cryosparc.com/application-guide/browsing-the-cryosparc-instance.md) - [Projects, Workspaces and Live Sessions](https://guide.cryosparc.com/application-guide/projects-workspaces-and-live-sessions.md) - [Jobs](https://guide.cryosparc.com/application-guide/jobs.md) - [Job Views: Cards, Tree, and Table](https://guide.cryosparc.com/application-guide/job-views-cards-tree-and-table.md) - [Creating and Running Jobs](https://guide.cryosparc.com/application-guide/creating-and-running-jobs.md): Working with the Job Builder, Job Cart and Job Quick Actions. - [Inspecting Job Data](https://guide.cryosparc.com/application-guide/inspecting-job-data.md) - [Low Level Results Interface](https://guide.cryosparc.com/application-guide/low-level-results-interface.md) - [Filters and Sorting](https://guide.cryosparc.com/application-guide/filters-and-sorting.md) - [View Options](https://guide.cryosparc.com/application-guide/view-options.md) - [Tags](https://guide.cryosparc.com/application-guide/tags.md) - [Flat vs Hierarchical Navigation](https://guide.cryosparc.com/application-guide/flat-vs-hierarchical-navigation.md) - [File Browser](https://guide.cryosparc.com/application-guide/file-browser.md): When selecting a path to create a project or input for a job parameter, CryoSPARC will display an integrated file browser. - [Blueprints](https://guide.cryosparc.com/application-guide/blueprints.md) - [Workflows](https://guide.cryosparc.com/application-guide/workflows.md) - [Managing Jobs](https://guide.cryosparc.com/application-guide/managing-jobs.md) - [Interactive Jobs](https://guide.cryosparc.com/application-guide/interactive-jobs.md) - [Upload Local Files](https://guide.cryosparc.com/application-guide/upload-local-files.md): Upload files from your local computer to CryoSPARC directly in the browser - [Managing Data](https://guide.cryosparc.com/application-guide/managing-data.md) - [Downloading and Exporting Data](https://guide.cryosparc.com/application-guide/downloading-and-exporting-data.md) - [Instance Management](https://guide.cryosparc.com/application-guide/instance-management.md) - [Admin Panel](https://guide.cryosparc.com/application-guide/admin-panel.md) - [Keyboard Shortcuts](https://guide.cryosparc.com/application-guide/keyboard-shortcuts.md) - [Image Formation](https://guide.cryosparc.com/cryo-em-foundations/image-formation.md) - [Contrast in Cryo-EM](https://guide.cryosparc.com/cryo-em-foundations/image-formation/contrast-in-cryo-em.md): Where does contrast in an electron micrograph come from? What can we do to produce more contrast? What effects do we have to take into account when processing data from electron micrographs? - [Waves as Vectors](https://guide.cryosparc.com/cryo-em-foundations/image-formation/waves-as-vectors.md) - [Aliasing](https://guide.cryosparc.com/cryo-em-foundations/image-formation/aliasing.md) - [Expectation Maximization in Cryo-EM](https://guide.cryosparc.com/expectation-maximization-in-cryo-em.md): An overview of the expectation maximization algorithm. - [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): Homogeneous reconstruction only (no alignment). - [Job: Heterogeneous Reconstruction Only](https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/3d-refinement/job-heterogeneous-reconstruction-only.md): Reconstruct class volumes from heterogeneous refinement or 3D classification - [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. - [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. - [About CryoSPARC Live](https://guide.cryosparc.com/live/about-cryosparc-live.md): From microscope to structure, in minutes. The fastest, streamlined path to high-resolution structures, during data collection or afterwards. - [Prerequisites and Compute Resources Setup](https://guide.cryosparc.com/live/prerequisites-and-compute-resources-setup.md) - [How to Access CryoSPARC Live](https://guide.cryosparc.com/live/how-to-access-cryosparc-live.md): CryoSPARC Live is automatically installed alongside CryoSPARC. - [UI Overview](https://guide.cryosparc.com/live/ui-overview.md): CryoSPARC Live UI Overview - [New Live Session: Start to Finish Guide](https://guide.cryosparc.com/live/new-live-session-start-to-finish-guide.md) - [CryoSPARC Live Tutorial Videos](https://guide.cryosparc.com/live/tutorial-videos.md) - [Live Jobs and Session-Level Functions](https://guide.cryosparc.com/live/live-jobs-and-session-level-functions.md): Overview of CryoSPARC Live architecture and job types specific to Live. - [Performance Metrics](https://guide.cryosparc.com/live/performance-metrics.md) - [Managing a CryoSPARC Live Session from the CLI (≤v4.7)](https://guide.cryosparc.com/live/managing-a-cryosparc-live-session-from-the-cli.md): This guide details how to automate the creation, configuration and overall management of a CryoSPARC Live session in Python via the CryoSPARC API. - [Managing a CryoSPARC Live Session from the CLI (v5.0+)](https://guide.cryosparc.com/live/managing-a-cryosparc-live-session-from-the-cli-v5.0.md) - [FAQs and Troubleshooting](https://guide.cryosparc.com/live/faqs-and-troubleshooting.md) - [v3 User Interface Guide](https://guide.cryosparc.com/guides-for-v3/user-interface-and-usage-guide.md): The information in this section applies to CryoSPARC ≤v3.3. - [Dashboard](https://guide.cryosparc.com/guides-for-v3/user-interface-and-usage-guide/dashboard.md) - [Project and Workspace Management](https://guide.cryosparc.com/guides-for-v3/user-interface-and-usage-guide/project-and-workspace-management.md) - [Create and Build Jobs](https://guide.cryosparc.com/guides-for-v3/user-interface-and-usage-guide/create-and-build-jobs.md) - [Queue Job, Inspect Job and Other Job Actions](https://guide.cryosparc.com/guides-for-v3/user-interface-and-usage-guide/queue-job-inspect-job-and-other-job-actions.md) - [View and Download Results](https://guide.cryosparc.com/guides-for-v3/user-interface-and-usage-guide/view-and-download-results.md) - [Job Relationships](https://guide.cryosparc.com/guides-for-v3/user-interface-and-usage-guide/job-relationships.md) - [Resource Manager](https://guide.cryosparc.com/guides-for-v3/user-interface-and-usage-guide/resource-manager.md) - [User Management](https://guide.cryosparc.com/guides-for-v3/user-interface-and-usage-guide/user-management.md) - [Tutorial: Job Builder](https://guide.cryosparc.com/guides-for-v3/job-builder-tutorial.md): An in-depth explanation of CryoSPARC's Job Builder, inputs and outputs. - [Get Started with CryoSPARC: Introductory Tutorial (v3)](https://guide.cryosparc.com/guides-for-v3/cryo-em-data-processing-in-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: Manually Curate Exposures (v3)](https://guide.cryosparc.com/guides-for-v3/tutorial-manually-curate-exposures.md): Manually Curate Exposures is an interactive job in CryoSPARC that enables a user to visually inspect and curate a set of micrographs or movies. This tutorial refers to CryoSPARC v3.3 and earlier. - [Guide: Data Management in CryoSPARC (≤v3.3)](https://guide.cryosparc.com/guides-for-v3/tutorial-data-management-in-cryosparc.md): An overview of all data management utilities and common use cases. - [Questions and Support](https://guide.cryosparc.com/resources/questions-and-support.md): How to get help for CryoSPARC. --- # Agent Instructions This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com. ## Querying This Documentation If you need additional information, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on a page URL with the `ask` query parameter: ``` GET https://guide.cryosparc.com/readme.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.