CryoSPARC Guide
  • About CryoSPARC
  • Current Version
  • Licensing
    • Non-commercial license agreement
  • Setup, Configuration and Management
    • CryoSPARC Architecture and System Requirements
    • CryoSPARC Installation Prerequisites
    • How to Download, Install and Configure
      • Obtaining A License ID
      • Downloading and Installing CryoSPARC
      • CryoSPARC Cluster Integration Script Examples
      • Accessing the CryoSPARC User Interface
    • Deploying CryoSPARC on AWS
      • Performance Benchmarks
    • Using CryoSPARC with Cluster Management Software
    • Software Updates and Patches
    • Management and Monitoring
      • Environment variables
      • (Optional) Hosting CryoSPARC Through a Reverse Proxy
      • cryosparcm reference
      • cryosparcm cli reference
      • cryosparcw reference
    • Software System Guides
      • Guide: Updating to CryoSPARC v4
      • Guide: Installation Testing with cryosparcm test
      • Guide: Verify CryoSPARC Installation with the Extensive Validation Job (v4.3+)
      • Guide: Verify CryoSPARC Installation with the Extensive Workflow (≤v4.2)
      • Guide: Performance Benchmarking (v4.3+)
      • Guide: Download Error Reports
      • Guide: Maintenance Mode and Configurable User Facing Messages
      • Guide: User Management
      • Guide: Multi-user Unix Permissions and Data Access Control
      • Guide: Lane Assignments and Restrictions
      • Guide: Queuing Directly to a GPU
      • Guide: Priority Job Queuing
      • Guide: Configuring Custom Variables for Cluster Job Submission Scripts
      • Guide: SSD Particle Caching in CryoSPARC
      • Guide: Data Management in CryoSPARC (v4.0+)
      • Guide: Data Cleanup (v4.3+)
      • Guide: Reduce Database Size (v4.3+)
      • Guide: Data Management in CryoSPARC (≤v3.3)
      • Guide: CryoSPARC Live Session Data Management
      • Guide: Manipulating .cs Files Created By CryoSPARC
      • Guide: Migrating your CryoSPARC Instance
      • Guide: EMDB-friendly XML file for FSC plots
    • Troubleshooting
  • Application Guide (v4.0+)
    • A Tour of the CryoSPARC Interface
    • Browsing the CryoSPARC Instance
    • Projects, Workspaces and Live Sessions
    • Jobs
    • Job Views: Cards, Tree, and Table
    • Creating and Running Jobs
    • Low Level Results Interface
    • Filters and Sorting
    • View Options
    • Tags
    • Flat vs Hierarchical Navigation
    • File Browser
    • Blueprints
    • Workflows
    • Inspecting Data
    • Managing Jobs
    • Interactive Jobs
    • Upload Local Files
    • Managing Data
    • Downloading and Exporting Data
    • Instance Management
    • Admin Panel
  • Cryo-EM Foundations
    • Image Formation
      • Contrast in Cryo-EM
      • Waves as Vectors
      • Aliasing
  • Expectation Maximization in Cryo-EM
  • Processing Data in cryoSPARC
    • Get Started with CryoSPARC: Introductory Tutorial (v4.0+)
    • Tutorial Videos
    • All Job Types in CryoSPARC
      • Import
        • Job: Import Movies
        • Job: Import Micrographs
        • Job: Import Particle Stack
        • Job: Import 3D Volumes
        • Job: Import Templates
        • Job: Import Result Group
        • Job: Import Beam Shift
      • Motion Correction
        • Job: Patch Motion Correction
        • Job: Full-Frame Motion Correction
        • Job: Local Motion Correction
        • Job: MotionCor2 (Wrapper) (BETA)
        • Job: Reference Based Motion Correction (BETA)
      • CTF Estimation
        • Job: Patch CTF Estimation
        • Job: Patch CTF Extraction
        • Job: CTFFIND4 (Wrapper)
        • Job: Gctf (Wrapper) (Legacy)
      • Exposure Curation
        • Job: Micrograph Denoiser (BETA)
        • Job: Micrograph Junk Detector (BETA)
        • Interactive Job: Manually Curate Exposures
      • Particle Picking
        • Interactive Job: Manual Picker
        • Job: Blob Picker
        • Job: Template Picker
        • Job: Filament Tracer
        • Job: Blob Picker Tuner
        • Interactive Job: Inspect Particle Picks
        • Job: Create Templates
      • Extraction
        • Job: Extract from Micrographs
        • Job: Downsample Particles
        • Job: Restack Particles
      • Deep Picking
        • Guideline for Supervised Particle Picking using Deep Learning Models
        • Deep Network Particle Picker
          • T20S Proteasome: Deep Particle Picking Tutorial
          • Job: Deep Picker Train and Job: Deep Picker Inference
        • Topaz (Bepler, et al)
          • T20S Proteasome: Topaz Particle Picking Tutorial
          • T20S Proteasome: Topaz Micrograph Denoising Tutorial
          • Job: Topaz Train and Job: Topaz Cross Validation
          • Job: Topaz Extract
          • Job: Topaz Denoise
      • Particle Curation
        • Job: 2D Classification
        • Interactive Job: Select 2D Classes
        • Job: Reference Based Auto Select 2D (BETA)
        • Job: Reconstruct 2D Classes
        • Job: Rebalance 2D Classes
        • Job: Class Probability Filter (Legacy)
        • Job: Rebalance Orientations
        • Job: Subset Particles by Statistic
      • 3D Reconstruction
        • Job: Ab-Initio Reconstruction
      • 3D Refinement
        • Job: Homogeneous Refinement
        • Job: Heterogeneous Refinement
        • Job: Non-Uniform Refinement
        • Job: Homogeneous Reconstruction Only
        • Job: Heterogeneous Reconstruction Only
        • Job: Homogeneous Refinement (Legacy)
        • Job: Non-uniform Refinement (Legacy)
      • CTF Refinement
        • Job: Global CTF Refinement
        • Job: Local CTF Refinement
        • Job: Exposure Group Utilities
      • Conformational Variability
        • Job: 3D Variability
        • Job: 3D Variability Display
        • Job: 3D Classification
        • Job: Regroup 3D Classes
        • Job: Reference Based Auto Select 3D (BETA)
        • Job: 3D Flexible Refinement (3DFlex) (BETA)
      • Postprocessing
        • Job: Sharpening Tools
        • Job: DeepEMhancer (Wrapper)
        • Job: Validation (FSC)
        • Job: Local Resolution Estimation
        • Job: Local Filtering
        • Job: ResLog Analysis
        • Job: ThreeDFSC (Wrapper) (Legacy)
      • Local Refinement
        • Job: Local Refinement
        • Job: Particle Subtraction
        • Job: Local Refinement (Legacy)
      • Helical Reconstruction
        • Helical symmetry in CryoSPARC
        • Job: Helical Refinement
        • Job: Symmetry search utility
        • Job: Average Power Spectra
      • Utilities
        • Job: Exposure Sets Tool
        • Job: Exposure Tools
        • Job: Generate Micrograph Thumbnails
        • Job: Cache Particles on SSD
        • Job: Check for Corrupt Particles
        • Job: Particle Sets Tool
        • Job: Reassign Particles to Micrographs
        • Job: Remove Duplicate Particles
        • Job: Symmetry Expansion
        • Job: Volume Tools
        • Job: Volume Alignment Tools
        • Job: Align 3D maps
        • Job: Split Volumes Group
        • Job: Orientation Diagnostics
      • Simulations
        • Job: Simulate Data (GPU)
        • Job: Simulate Data (Legacy)
    • CryoSPARC Tools
    • Data Processing Tutorials
      • Case study: End-to-end processing of a ligand-bound GPCR (EMPIAR-10853)
      • Case Study: DkTx-bound TRPV1 (EMPIAR-10059)
      • Case Study: Pseudosymmetry in TRPV5 and Calmodulin (EMPIAR-10256)
      • Case Study: End-to-end processing of an inactive GPCR (EMPIAR-10668)
      • Case Study: End-to-end processing of encapsulated ferritin (EMPIAR-10716)
      • Case Study: Exploratory data processing by Oliver Clarke
      • Tutorial: Tips for Membrane Protein Structures
      • Tutorial: Common CryoSPARC Plots
      • Tutorial: Negative Stain Data
      • Tutorial: Phase Plate Data
      • Tutorial: EER File Support
      • Tutorial: EPU AFIS Beam Shift Import
      • Tutorial: Patch Motion and Patch CTF
      • Tutorial: Float16 Support
      • Tutorial: Particle Picking Calibration
      • Tutorial: Blob Picker Tuner
      • Tutorial: Helical Processing using EMPIAR-10031 (MAVS)
      • Tutorial: Maximum Box Sizes for Refinement
      • Tutorial: CTF Refinement
      • Tutorial: Ewald Sphere Correction
      • Tutorial: Symmetry Relaxation
      • Tutorial: Orientation Diagnostics
      • Tutorial: BILD files in CryoSPARC v4.4+
      • Tutorial: Mask Creation
      • Case Study: Yeast U4/U6.U5 tri-snRNP
      • Tutorial: 3D Classification
      • Tutorial: 3D Variability Analysis (Part One)
      • Tutorial: 3D Variability Analysis (Part Two)
      • Tutorial: 3D Flexible Refinement
        • Installing 3DFlex Dependencies (v4.1–v4.3)
      • Tutorial: 3D Flex Mesh Preparation
    • Webinar Recordings
  • Real-time processing in cryoSPARC Live
    • About CryoSPARC Live
    • Prerequisites and Compute Resources Setup
    • How to Access cryoSPARC Live
    • UI Overview
    • New Live Session: Start to Finish Guide
    • CryoSPARC Live Tutorial Videos
    • Live Jobs and Session-Level Functions
    • Performance Metrics
    • Managing a CryoSPARC Live Session from the CLI
    • FAQs and Troubleshooting
  • Guides for v3
    • v3 User Interface Guide
      • Dashboard
      • Project and Workspace Management
      • Create and Build Jobs
      • Queue Job, Inspect Job and Other Job Actions
      • View and Download Results
      • Job Relationships
      • Resource Manager
      • User Management
    • Tutorial: Job Builder
    • Get Started with CryoSPARC: Introductory Tutorial (v3)
    • Tutorial: Manually Curate Exposures (v3)
  • Resources
    • Questions and Support
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On this page
  • Selecting Jobs
  • Job Info Tags
  • Inspecting Jobs
  • Event Log
  • Interactive
  • Inputs and Parameters
  • Outputs
  • Volumes
  • Metadata
  • Related Jobs
  • Comparing Jobs
  1. Application Guide (v4.0+)

Inspecting Data

PreviousWorkflowsNextManaging Jobs

Last updated 1 year ago

Selecting Jobs

The sidebar automatically displays information pertaining to the selected jobs. Click to select a job, use the arrow keys to navigate between jobs, and press command +click to add or remove jobs from your selection.

Job Info Tags

Almost all jobs include summary information presented on the cards, table, and tree view - these are called info tags. For example, the Blob Picker job card now displays key information in tags anchored around the preview images to display the minimum and maximum diameter configured, how many micrographs were processed, how many particles were picked, and the average number of particles picked per micrograph:

The combination of job preview images, info tags, and additional metadata displayed on the job card footer makes it easier to distinguish between multiple runs of the same job type with different parameters and results.

Inspecting Jobs

You can inspect a job to view much more information about a job including a real-time log of events and interactive utilities. To inspect a job, select it and press spacebar or click on the ‘View Job’ button from the sidebar or click on the job ID and type on the header of the job card.

The job preview dialog opens above the current page and can be dismissed at any time by pressing the spacebar or escape key or clicking on the ‘x’ button.

At the top of the job inspection dialog is a breadcrumbs element depicting the hierarchy of a job. Clicking on a project or workspace will navigate to that page. Clicking on the job will navigate to the workspace page and scroll to that job.

Alongside the breadcrumbs, you can star the job and view the elapsed time.

The bottom of the dialog contains a footer with helpful information such as what processing node the job was queued on, how many GPUs were allocated and what custom parameters were set:

The job inspection dialog is comprised of various tabs that provide more detail into the processing history and results of the job. To the right of the dialog’s main content area is a collapsible sidebar that lists all output groups the job produces. From this sidebar you can drag and drop output groups into the job builder or download results.

Close the sidebar (top-right button or command + /) to expand the visible area of the job inspection dialog.

Event Log

As a job runs, events are published in real-time as a job processes. Events are viewable when a job completes. Above the log, a list of controls are available:

  • Show from top: Jump to the top of the event log, scroll to load events in chronological order.

  • Follow latest: Skip to the last available checkpoint and listen for new events.

  • Select a checkpoint: View a list of checkpoints and timestamps, click to jump to the start of the checkpoint.

  • Filter types: Display events of a certain type (such as text or image).

  • Filter flags: Display events of a certain job-dependent flag (such as central slices or FSC curves).

  • Show CPU usage: Display CPU memory usage of the processing node alongside each log.

  • Show timestamps: Display a timestamp alongside each log (you can also hover over the icon on the left side of each log to view the timestamp).

Interactive

The interactive tab is only visible when running an interactive job that is in ‘waiting’ status. Please refer to the Interactive Jobs guide to learn more.

Inputs and Parameters

In addition to the details sidebar, this tab displays all inputs and parameters that were configured. Select 'Show slots' to view low-level slots contained within each input group. Parameters will be marked as either default (grey/blue) or custom (green). Advanced parameters are denoted with an ‘A’. You can toggle between listing only custom parameters or all parameters.

Outputs

In addition to the output groups sidebar panel, the outputs tab displays a comprehensive overview of all the output groups and individual outputs a job creates. Please refer to the Job Builder Tutorial to learn more about how you can take advantage of the low-level results CryoSPARC generates.

Volumes

This tab is only visible when a job outputs one or more volumes. By selecting a volume from the left sidebar, it will load in the integrated volume viewer. You can set a threshold, zoom and pan, start or pause animation, and download the volume for inspection in an external software.

For volumes that also have an associated colour map (such as running a refined volume through Local Resolution Estimation), an additional option will become available in the sidebar to view the coloured volume.

Metadata

Useful for when archiving or debugging, the metadata tab contains all job data stored in the database. You can search for specific fields using the search bar. The path to the job logs location on disk is listed as well and can be clicked to copy.

In addition to the job data, you can view the text log of the job by clicking on the ‘Log’ sub-tab:

Related Jobs

When a job is selected or inspected, the sidebar details panel will list an overview of what other jobs are connected to it via parent or children connections, or it being cloned from another job of the same type. Hovering over each job will display a tooltip containing an outline of that job, including what parameters it has been configured with. Clicking on a related job will inspect it. To open the related job in a new tab, click it while pressing the command (macOS) or control (Windows, Linux) key.

Comparing Jobs

In CryoSPARC v4.0, you can command + click to select multiple jobs. This will show a unique sidebar panel where each job presented as a card with identifying details. To compare the selected jobs, press the spacebar key or click on “Compare Jobs” from the sidebar:

The comparison dialog is an easy way to view differences between two or more jobs that may be located in different workspaces or projects. Each parameter listed can be clicked to copy it to your clipboard.

Selecting a single job will display its details in the sidebar ‘Details’ panel. You can press Spacebar, ‘View Job’ or click the job ID/type on the header of the card.
Inspecting a completed 2D Classification job presents the Event Log tab for quick inspection of the latest events.
You can close the job inspection dialog by clicking on the ‘X’ button on the top-right of the dialog or press the Spacebar or Escape key
The job dialog footer contains metadata with additional details visible when hovered.
Viewing a selection of related jobs connected to a Homogeneous Refinement
Each related job will display key information about its configuration and outputs