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
  • Cards View
  • Navigation
  • Filters
  • Tree View
  • Navigation and Selection
  • Filters
  • Dependent Jobs
  • Shortcuts
  • Table View
  • Job Groups
  • Creating Groups
  • Selecting Groups
  • Expanding and Collapsing Groups
  • Adding Jobs to a Group
  • Removing Jobs from a Group
  • Removing a Group
  • Navigating to a Group
  • Missing Connections
  • Shortcuts
  1. Application Guide (v4.0+)

Job Views: Cards, Tree, and Table

PreviousJobsNextCreating and Running Jobs

Last updated 8 months ago

Cards View

Job cards in CryoSPARC are displayed by default in a masonry grid referred to as the “Cards View”. Cards are laid out from left to right and then in sequential rows organized by a sort attribute and sort order. The default sort attribute is the “Date Created”, and the default sort order is ascending (this means the most recent jobs will appear at the bottom of the view, while the oldest will appear at the top).

Navigation

The cards view is a scrollable page that progressively loads job information as you navigate. This means that you can use the scroll bar or your mouse wheel to navigate to any point in the view, whether you are working on 100 jobs or 1000 jobs, without needing to change pages.

Targeting

The target button on the filter bar allows you to quickly navigate the view to the currently selected job. This can also be done by pressing the T key on your keyboard. The adjoined arrow button will open a dropdown menu with options for the “Last Running Job”, “Last Completed Job”, or “Last Created Job”. Selecting an option from this menu will select the corresponding job and then navigate you to it.

Searching

The job search menu can be opened by clicking on the job count button in the footer. This menu contains a list of jobs in the current view (workspace, project, or instance). The menu items include a colour indicator for the job’s current status, as well as its job ID and job type. The list can be filtered by typing into the input at the bottom of the menu. Clicking on a job in this list will select the job and then immediately navigate you to it.

The job search menu is limited to the first 1000 jobs in the view, sorted by the attribute and order that you have selected.

Filters

Tree View

The tree view is a unique view available for jobs inside of a workspace or project. This view lays out all jobs as an interconnected network branching out from the first job(s) in the processing pipeline. Each job is linked to previous and subsequent jobs with coloured lines representing the flow of inputs and outputs between them.

The tree view is in many ways a “superset” of the cards view, which is to say that the job cards themselves look and behave for all intents and purposes identically to the card view, and jobs also retain all of the same information and actions. All systems available in the card view for navigation (ie. targeting and searching) are also available in the tree view.

Navigation and Selection

When initially navigating into the tree view, the view will load with all jobs visible and centred horizontally and vertically within the viewing area. The scroll wheel is set to zoom in and out of the view by default, and you can click and drag anywhere in the viewing area to navigate.

Zoom and Pan

The zoom or pan modes are shown in the bottom right of the view, as the magnifying glass and four-arrows icons respectively. These control the scroll behaviour. In zoom mode (default), scrolling will zoom the view in or out, while in pan mode, scrolling will pan the view horizontally or vertically. Holding the command/ ctrl key while scrolling will invert the action. For example, by holding down the command key while in zoom mode, scrolling would cause the view to pan instead. Both options are also mapped to their own keyboard shortcuts. Zoom mode is mapped to the Z key while pan mode is mapped to the X key beside it.

Drag and Select

The two options for the click mode, drag and select, are shown in the bottom right of the view as the hand and pointer icons respectively. By default, the click mode is set to drag. This mode allows you to click, hold, and drag the tree view to navigate around it. By switching to select mode you can click, hold, and drag the cursor to select multiple jobs in a rectangular selection box (much like drag selection of files on the desktop of most modern operating systems). Drag select will, by default, start a new selection each time you begin dragging the selection box. You can retain your current selection and select additional jobs by holding the command / ctrl key while making your selection. Drag mode is mapped to the C key while select mode is mapped to the V key.

Scale Levels

The scale switcher is located on the bottom left of the viewing area and allows you to reset the view to show all of the available jobs, select a custom zoom level, and cycle through multiple preset zoom levels. The R key will reset the view, while holding the shift key and then pressing the R key will cycle through the preset zoom levels.

Filters

Filters can be applied in the tree view in the same way as in the cards view, but in order to retain the spatial context of job trees, filtered jobs will still appear in the tree view in the same position but as dotted outlines, with no input or output connections.

Jobs that are not filtered out appear as usual and will have their input/output connections rendered if they connect to other jobs that have also not been filtered out.

Dependent Jobs

In order to correctly render the layout of the tree view, it is sometimes necessary to include job cards for jobs that are either not in the current workspace or have been deleted.

Jobs that are not in the current workspace but must be shown in the tree are referred to as “dependent” jobs. These jobs will appear with a solid orange border and an unlinked icon in their footer. They include two buttons that are visible on the card when it is hovered. These buttons allow you to link or move the job into the current workspace.

Dependent jobs cannot be selected or interacted with at all unless they have been linked or moved into the current workspace.

Shortcuts

Note: command key represents command on Mac and ctrl on Windows or Linux

  • Z key will set the scroll mode to zoom.

  • X key will set the scroll mode to pan.

  • C key will set the click mode to drag.

  • V key will set the click mode to select.

  • T will reset the view on the currently selected job or set of jobs.

  • R will reset the view to show all jobs.

  • shift + R will cycle through zoom levels (0.25x, 0.5x, 1x).

  • Holding the command key while scrolling will invert scroll mode to pan or zoom (depending on which is currently selected).

Table View

The table view presents jobs with their information laid out in a highly structured and predictable manner. The rows represent jobs, and the columns represent the different types of information that the jobs contain.

The table view is particularly useful for accounting purposes, as it allows you to view a condensed representation of you job data, much like a spreadsheet.

All of the filters and sorting options that are available in the card and tree view are available in the table view as well. Jobs can be quickly sorted by clicking the column header (eg. project, job, or status), which will set the sort attribute and the sort order, clicking the header again will invert the sort order.

Clicking a row will select the associated job, and clicking it again will deselect it. The checkbox at the far left of the row shows whether the job is selected or not (and can also be clicked to toggle the selection on or off).

The table view (as with the other views) can be saved as a CSV by clicking the download button at the bottom right of the jobs footer. This will export the entire data selection with the same filter, sorting, and granularity options as set in the table view.

Job Groups

Job groups are an organizational feature that allow you to collapse multiple jobs into a single card to maintain the legibility of a workspace. They are designed to compact branches of jobs that are not being used for active processing but are still required for reference or continued processing in the future.

Job groups are simple constructs that are meant to be created and deleted without much overhead. Options for a title and description allow you to clarify a group’s purpose, and can help to document the thought process behind branches of processing when coming back later.

Creating Groups

To create a group you must select all of the jobs you would like to have included in it. From here you can select the “Group Jobs” option from the job sidebar actions menu, or right click on any of the selected jobs to open the quick actions menu and select the option from there. Alternatively you can use the keyboard shortcut command + G . All of these options will open the job group dialog with fields available for a title, description, and colour. All of these fields are optional, and if you would prefer to leave them blank a default title and colour will be applied. Clicking the “Create Group” button at the bottom of the dialog will create the group (This button is focused by default when the dialog opens, allowing the group to be created with all default fields by pressing the enter key).

Selecting Groups

Groups can be selected by clicking on the group card or by clicking the group menu button on the footer to open the group search menu and choose the group you would like to select. This will also navigate the view to the selected group.

Groups are meant to be lightweight, and because of this, they do not have any specific metadata associated with them. When selecting a group you are essentially just selecting the jobs that are in that group. This is reflected in the sidebar, which is identical to the multi-selection sidebar that is shown when selecting multiple jobs whether they are grouped or not.

Expanding and Collapsing Groups

All groups, and jobs that belong to a group, will appear with a group widget on their card. This widget includes the group ID and a +/- button.

Clicking the +/- button will expand or collapse the group. Expanding the group will show all of the jobs contained in the group directly in the view, while collapsing the group will show only the group card. Keyboard shortcuts are also available for expanding and collapsing groups. When a group or group job is selected or hovered, you can press the E key to either expand or collapse it.

Clicking the group ID will select all of the jobs in the group, this allows you to select all grouped jobs whether they are collapsed into a group card or expanded as individual jobs.

The view footer also includes +/- toggle buttons beside the group count that allow you to expand or collapse all of the groups in the workspace.

Adding Jobs to a Group

You can add a single job or multiple jobs to an existing group by selecting the jobs and then right clicking any of them to open the quick actions menu. From here you can navigate to the “Add to Group” or “Add {x} Jobs to Group” option and select the group you wish to add these jobs to from the submenu.

Removing Jobs from a Group

You can remove any number of jobs from an existing group by selecting the jobs and then opening the quick actions menu by right clicking on any of them. From here you can select the “Remove From Group” or “Remove Jobs from Group” option. Alternatively you can use the command + shift + G keyboard shortcut to quickly remove jobs from a group. If you remove all of the jobs from a group, the group itself will automatically be removed.

Removing a Group

A group can be removed by hovering the group card to show its action buttons on the bottom right hand corner of the card, and then clicking the ungroup button. This will not delete the jobs within the group, only remove the group itself.

Navigating to a Group

Groups have all of the same navigation options as job cards. This means that a selected group or a selection of group jobs, can be automatically panned and zoomed to by clicking the target button on the filter bar (or by pressing the T key).

Groups can also be searched and found in the group menu to select and navigate to the group card or the expanded group job cards. This menu can be accessed by clicking the group menu button in the footer.

Missing Connections

A Job Group is simply a set of jobs. However, not every set of jobs can be made into a Job Group. For a set of jobs to be a valid group, the following rule must be true: For any two jobs in the set, all the jobs on the chain connecting those two jobs must also be inside the set.

This rule is a necessary condition in order for the Job Group to be rendered as a single card in the tree view and is therefore a requirement.

As the simplest example of this rule, consider a job chain A → B → C.

The set A,C is not a valid group, because B is on the chain connecting A and C. However, A,B, B,C, or A,B,C are valid groups.

When creating a group, adding jobs to a group, or removing jobs from a group, if the rule above is violated, a Missing Connections error will occur. Sometimes, with a large group or a complex tree, it is not easy to tell which jobs are causing the error.

When you encounter this error, we advise that you carefully inspect the selection of jobs that you have made, and make sure that you have not missed any jobs that are on chains between jobs that are inside the group. It is important to make sure to check for, and link or move, any “dependent” jobs from other workspaces that are needed in order to make a valid group into the current workspace.

Shortcuts

Note: command key represents command on Mac and ctrl on Windows or Linux

  • O will toggle the outputs view on all cards.

  • E will toggle the expanded/collapsed state of a group when selected or hovered (hover takes precedence).

  • T will navigate the view to the currently selected job or set of jobs.

  • command + G will group selected jobs.

  • command + shift + G will ungroup selected jobs.

A variety of filters are available to help you quickly and easily find sets of jobs that match a specific criteria (eg. jobs that were created between two dates, or have a specific job type). All jobs that match the filter will continue to be displayed, and those that do not will be removed from the view. Filters can be applied additively to create a more granular criteria for matching jobs (eg. all Ab-Initio jobs that have a status of completed or failed). More information on the filter system can be found in the "” section of the guide.

Filters and Sorting
Missing connection error and resolution when creating a group
Missing connection error and resolution when adding jobs to an existing group