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
Powered by GitBook
On this page
  • Accessing Tags
  • Applying Tags
  • Using Tags
  • Tag Management
  • Tag Use Cases
  1. Application Guide (v4.0+)

Tags

PreviousView OptionsNextFlat vs Hierarchical Navigation

Last updated 2 years ago

Tags enable a useful level of user-customizable organization in your CryoSPARC instance. Tags are shared among all users within the instance and can be customized with a title, description, and colour. There are two categories of tags, a 'general' type tag that can be applied to items of any type, and item-specific tags that only apply to either project, workspaces, sessions, or jobs.

The main purpose of tags are to allow you to quickly find and view specific subsets of data either inside of a container (projects or workspaces) or across the entire instance. This gives a lot of flexibility for creating arbitrary groupings of items that you want to be able to find again quickly or compare and reference.

Accessing Tags

The main access point for creating and navigating tags is the Quick Access Menu that can be expanded from the navigation bar on the left side of the app window. By clicking the “Tags” tab at the top of the menu you will be able to see all of the tags currently created in your instance. Each tag grouping is represented here in a collapsable drawer with the type of tag and total count of tags with that type shown on the drawer header. You can use the search bar at the top to filter the available tags and quickly find one that you are looking for. Beside the search bar there is a “+” button that will open the tag creation slide-over and allow you to create a new tag. Once created that new tag will be available to view and use. Each tag row in the menu shows the unique tag ID (e.g., T5, T20, etc.), the tag title, and a count of how many items have been given that tag (eg. a project tag of EMPIAR with a count of 10 has been assigned to 10 projects in the instance). Clicking on one of these rows will navigate you to the relevant view with a filter for that tag applied (in the case of general tags, a context menu will open when the row is clicked and allow you to select the type of item you want to view).

Applying Tags

Once tag(s) exist in the instance, they can be applied to any relevant item. There are multiple ways to apply a tag depending on how you are interacting with the item. Let’s look at applying a tag to a project as an example.

By navigating to the browse section we will see all of our projects in the cards view. We can choose a project to apply our tag to and use either the quick actions menu, or the sidebar to add it. Right clicking the card or clicking the triple dot menu in the header will open the quick actions menu, we can then navigate down to the “Edit tags” menu item and into the sub menu with a list of relevant tags. Project tags will appear first and general tags below. Each tag in the menu has the same information as the rows in the quick access menu, the ID, title, and a count of how many items that tag has been applied to. By clicking any tag in the menu (lets take our EMPIAR tag for example) that tag will be applied to the project. Opening the menu again and viewing the “Edit tags” submenu will show a checkmark on any tags that have been applied to the card (in this case EMPIAR). Clicking the tag row again will remove the tag from the project.

Tags can also be seen in the item sidebar, inside the “Details” panel (which is the first panel from the top). The tags row is just below the title row and displays all tags applied to the item. When this row is hovered, an edit button will appear, clicking this button will open the same “Edit tags” menu with the exact same functionality as the one available from the quick actions menu, discussed above.

Tags can be applied to projects, workspaces, sessions, and jobs in exactly the same way. The only difference is the granularity specific tags available.

Using Tags

As mentioned above, the main use for tags is organizing data into subsets that either compliment the existing project and workspace demarcations, or acts as a wider aggregator around them. Tags are fundamentally custom filters, and as such operate functionally within the filter system. The control bar has a “Tags” quick filter button above the main content area, where tag filters can be set and removed. Tag filters are also available in the filter bar menu with all other applicable filters.

Clicking the “Tags” quick filter button or entering the “Tags” filter submenu from the filter bar will open the same menu with identical functionality. Clicking on a tag in this menu will add a “Tags” filter group with the specific item applied. This will cause only items with this tag to be shown in the interface (eg. if you add the EMPIAR tag as a filter on the projects view, only projects with the EMPIAR tag applied to them will now show in the card grid). Adding additional tags is an additive filtering process and will show all items with any of the added tags applied to them.

Tag Management

Tags can be managed more comprehensively in the “Tags” tab of the manage dialog. Here all tags can be viewed in a table with all of their relevant information visible (ID, title, description, type, author, and date created). Each row in the table represents a separate tag and include a triple dot icon at the end of the row for accessing applicable actions for the tag, these include editing or deleting a tag.

Editing: Clicking the edit item in the triple dot tag row context menu will open the editing modal. Here you can change or tweak the title, update the description, and choose a new colour for the tag.

Deleting: Deleting a tag will remove it from the instance entirely, and remove it from all items it had been applied to. This is not reversible.

Tag Use Cases

  • Progression of a project by assigning various lifecycles (e.g., 'to-do', 'in-progress', 'done')

  • Denoting the type of microscope used to collect the data present in a project (e.g., 300KV, Krios)

  • Adding a demarcation of a quality result that can be referenced or returned to in the future (e.g., Good result)

  • Using a tag for reconstructions of a specific particle type that can be referenced together across the instance regardless of project (e.g., CoV S Protein tag)