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
  • Filter System
  • Quick Filter Buttons
  • Filter Bar
  • Sorting
  1. Application Guide (v4.0+)

Filters and Sorting

PreviousLow Level Results InterfaceNextView Options

Last updated 2 years ago

Cryo-EM data processing can become complex quickly. A large number of jobs, workspaces, and projects will be created in typical use. It therefore becomes very important to be able to filter and sort through items in CryoSPARC.

Filter System

When browsing CryoSPARC, the filter and sorting options are displayed in the control bar at the top of the main content area:

Quick Filter Buttons

Quick filter buttons help quickly filter the displayed items.

General Quick Filter Buttons

  • Starred: This button will toggle on the starred filter causing only starred items to be shown. This allows you to quickly locate the your important projects, workspaces, sessions, or jobs.

  • Mine: This filter will show only items created by you when toggled on. This can be useful if you are an admin user, or simply to filter out items shared with you to find your own data quickly and easily.

  • Tags: This filter will show all applicable tags with the granularity tags (eg. project or workspace specific tags) shown first, and general tags shown before. The numbers on the right side of each tag entry represent the number of items in the instance that have that tag applied.

Specific Quick Filter Buttons

  • Sessions

    • Status: The session status filter allows you to filter all sessions by running, completed, or paused. These filters are additive and adding more will show jobs of all selected status types.

  • Jobs

    • Status: The job status filter allows you to filter jobs by any available status, or combination of statuses. These include: Building, Queued, Launched, Started, Waiting, Running, Killed, Completed, and/or Failed.

Filter Bar

The filter bar is where more advanced filter compositions can be created and managed. It contains all possible filter options. In order to access the filter bar, you must click the “Filters” button on the control bar to open the underslung module.

Overview

The filter bar is a powerful system for adding, composing, and managing filters. The filter bar has separate filter options relevant to the type of item being filtered.

Filters that you apply are stored in the browser URL bar. This means that you can bookmark or copy the URL from the browser and return to any filtered view that you have created. You can also share the URL with other users who have access to the same projects, and they will see the same filtered view that you have created.

Walkthrough

The filter bar is composed of three parts: the filter button, input, and clear button. Clicking the filter button or in input area will open the filter options menu. In the input area, you can also type a word or phrase in order to quickly chose an attribute by which to filter. The clear button allows you to clear all of the filters in the bar in one action, reseting the filter state and showing all available items in the view below.

After opening the filter options menu, you can enter the menu by moving the cursor over it or pressing the down arrow on your keyboard.

There are three classes of filters: singular, compound, and toggle filters. Singular filters such as user filters have multiple options, but can only have one option active at a time. Compound filters such as tags, job type, or status, allow you to select multiple options and will additively filter results (eg. adding multiple status filter options, such as building, queued, and completed, will show all jobs that have any of those statuses).

Let’s begin by adding a building job status filter to see the resulting filter bar composition. After selecting the building status, the menu will remain open in order to allow you to add other status filters more easily. Click outside of the menu or press the escape key to close it.

Now that the filter has been added, it will appear in the input section of the filter bar. The light grey grouping indicator on the lefthand side of the filter tag shows the type of the filter added, in this case “Status”. The coloured filter tag on the righthand side shows the filter option that has been added, in this case “building”. By hovering over the filter tag a small red “X” indicator will show up on the top left corner of the tag, when clicked this will clear that particular filter option. Alternatively, hovering the grey filter grouping indicator on the lefthand side will also show a red “X” indicator on its top left corner, clicking this will clear all filters within that group.

Reopen the filter menu by clicking on the filter bar input section again (anywhere to the right of the currently existing tags). Add the status “killed” from the statuses submenu. This will add a second filter option to the statuses grouping.

Now all jobs shown will either be in building status or killed status. Additional filters from different groupings can be added, such as a date filter, or job type filter, to further isolate results.

Filters can be added and removed to compose a variety of specific views allowing you to find jobs quickly and easily, or compose sets of results outside of the constraints of project or workspace groupings. This can be especially powerful when adding tags or starred filters, which operate as higher level selection groupings similar to upper level granularity groupings but with more flexibility.

Sorting

Sorting options are located in the sort toggle button on the control bar beside the filter button. The sort button is composed of two parts, the sort order toggle on the lefthand side allows you to toggle ascending or descending order, and the sort option menu on the righthand side allows you to select what option you would like to sort by. By default, items are sorted by the “Date created” option. Projects and workspaces are sorted by default in descending order (showing the newest items at the top), while jobs are sorted in ascending order (showing the newest jobs at the bottom).

Like filters, sort options are stored in the browser URL, and therefore are retained when bookmarking or copying/sharing the URL.