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
  • Navigation
  • Item Cards
  • Quick Switchers
  • Quick Access Menu
  • Spotlight
  • Views
  • Cards View
  • Table View
  • Tree View
  1. Application Guide (v4.0+)

Browsing the CryoSPARC Instance

PreviousA Tour of the CryoSPARC InterfaceNextProjects, Workspaces and Live Sessions

Last updated 8 months ago

In order to interact with CryoSPARC and process data, you will need to browse the instance, navigating through the various projects, workspaces, sessions, and jobs that you and other users in the instance create. The Browse System is a set of tools and interfaces that help move around the instance and find the items you are looking for.

The browse system contains five fundamental components:

  1. Browse Header: The header sits above the main working area and provides options for high level navigation and creation.

  2. Control Bar: The control bar is where all actions involved in filtering, sorting, or setting a view option reside.

  3. Content Area: The main space in the browse system is the content area. This is where projects, workspaces, sessions, and jobs are shown in either card, table, or tree view.

  4. Footer: The footer shows total counts, curated filter options, and can be toggled using the footer switch button on the far left of the bar to show general active job and target information.

  5. Sidebar: The sidebar shows contextual information and applicable actions for any selected items.

From the CryoSPARC dashboard, browsing the instance begins with clicking on the container icon in the left-side navigation bar. This button brings you to the project cards view, showing all projects you have access to across the instance.

Navigation

Item Cards

When browsing through projects, workspaces, sessions, and jobs, each item will be displayed as a card by default.

Projects, workspaces, and sessions have buttons at the bottom of the card which can be clicked to open that item and navigate into a view of its contents. Jobs cards can be opened by clicking on the actionable header button which will expand the job inspection dialog.

Each type of card can also be selected by clicking on it, which will highlight it in blue and populate the sidebar with its information. From here the item can also be entered by clicking the “View” button at the bottom of the sidebar, or by pressing the enter key on your keyboard for projects, workspaces, and sessions, or the spacebar for jobs.

Quick Switchers

The quick switchers at the top left of the page indicate your current location within the instance, and allow for quickly entering, exiting, and switching between projects, workspaces, and sessions. The solid blue switcher indicates the type of items you are currently looking at in the main content area.

These switchers can be used to quickly jump around the instance by clicking the arrow button on the righthand side of the switcher to open the selection dropdown.

Once you navigate inside a project, workspace or session, an “X” button will appear on the lefthand side of the corresponding switcher. Clicking the “X” button will deselect the option and navigate you back up one level of navigation, while clicking the name will reopen the selection menu and allow the quick selection of a different option.

Quick Access Menu

The Quick Access Menu is available by clicking on the menu icon in the bottom left corner of the page.

The menu is composed of three tabs: Recent, Starred, and Tags. Use these menus to quickly jump to important items in your instance.

  • Recent: recently accessed items. Clicking on a project or workspace will open it and navigate you into the relevant section of the browse system. Clicking a session will navigate you into that session in the CryoSPARC Live view. Clicking a job will open its dialog without navigating away from your current location.

  • Starred: items that you have starred. Starring items can be done directly from the items card’s header, and for jobs can be done in the header section of their dialog as well.

  • Tags: all of the available tags across the instance along with counts of how many items they have been applied to. Clicking items will send you to a browse view with the selected tag applied as a filter. This quick access menu tab is covered in more depth in the “Tags” section below.

The last menu tab you accessed is remembered by the browser in the current browser tab until closed. This is in order to aid in navigating swiftly between items even when closing and reopening the menu. Each sub section inside of each menu tab is a drawer that can be closed by clicking the section header (e.g., Recent Projects). When an item is closed it will remain closed between browser tabs and even if the browser is closed and reopened. This allows you to organize each tab of the quick access menu to only show the items that are most important to you.

Spotlight

The spotlight allows unrestricted navigation through the interface and can be opened by clicking the magnifying glass icon in the navigation bar, the search bar button on the home page header, or by pressing the command + k keys together on the keyboard.

The spotlight input is automatically focused and you can begin typing into it immediately. Many commands are available, such as creating a new item, opening the jobs builder, or attaching a project.

Commands specifically for navigation include viewing all items in a granularity, or typing in the name of a project, workspace, or session to quickly find and open them.

Views

When browsing the CryoSPARC instance, you can select a view from the buttons in the top right corner of the content area.

Cards View

Items in CryoSPARC display as cards by default. Each card includes a header with the ID and title of the item along with action buttons for opening the card’s action menu and starring the item.

The card can be selected by clicking on it anywhere that is not an actionable button. This will add a blue selection outline to the card and add all of its relevant information to the sidebar. Once selected, the item can be opened by pressing the enter button on your keyboard (for projects, workspaces, and sessions). Items can also be opened by clicking the “view” button(s) at the bottom of their respective card, or by clicking the view button at the bottom of the active sidebar. Entering the selected item will navigate into the item and show all of its contained items (eg. entering a project will navigate to the workspaces view and show all of the workspaces belonging to that project). For jobs, selected cards can be opened by pressing the spacebar to expand the corresponding job dialog. Job cards can also be opened by clicking the card header button with the job ID and name.

Table View

The table view organizes each item as a row in a table. This can be particularly useful for getting an overview of large numbers of items and for accounting purposes. When the row is selected it will highlight blue and can be opened the same way as with a card, by pressing the enter button on your keyboard or by clicking the view button at the bottom of the sidebar. The download button at the bottom right of the jobs footer allows for exporting the entire data selection with the same filter, sorting, and granularity options as the table view in a CSV file.

Tree View

The tree view is a unique view only 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 by coloured lines representing the flow of inputs and outputs between jobs.

Navigate the tree view using the two control palettes present in the bottom left and right corners of the viewing area. Zooming is the default scroll-wheel behaviour, which can be changed by clicking the “pan” icon in the bottom right corner of the tree view. Default zoom levels are shown in the bottom left corner of the viewing area. These can be used to quickly toggle between different levels of zoom to quickly move the entire view in or out to a set scale factor. When first switching to the tree view, all trees will be centred within the view both vertically and horizontally, making it easy to locate your data immediately upon entry.

Tree view job cards contain a more condensed version of the job data available in the standard cards view. Available actions are shown on hover in a command palette located in the bottom righthand corner of each card. Right clicking the card will show the quick actions menu just like cards from the card view and rows in the table view. Additional information is shown in a tooltip that will appear above the card when it is hovered for a short period of time. These tooltips along with the quick actions menu make it easier to see relevant job details and act on the job without needing to change your zoom level in order to do so.

Due to the unique structure of the tree view, sorting actions cannot be applied in this view.