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OPS Explorer Quickstart

Use the Explorer

A short, visual tour of the viewer for first-time users. For full reference detail, see the Comprehensive Reference for the OPS Explorer.

Contents

Tour of the Viewer

From the OPS Explorer about page, click Explore on any collection to open the viewer full-screen.

The viewer is split into two regions:

Default two-panel viewer layout: left control panel with Gene Knockouts and tabs, right visualization area with embedding and images panels

Region What it does
Left Panel (control center) Search gene knockouts, manage panels, apply coloring
Visualization Panels (right side, 1–4 panels) Show embeddings, fluorescence images, and volcano plots

Hovering or clicking a dot in any visualization panel highlights the same gene knockout across every other open panel simultaneously.

Note: In this viewer, each dot is one gene knockout - not a cell. This is different from CellxGene, where each dot is one cell. Hovering on a dot will show how many cells there are for that gene KO. Only the volcano plot generated with CROP-seq data (shown below) is where each dot is a measured gene.

Left Panel

The left panel has two regions:

Left panel with top region showing search and gene knockouts selected; bottom region with tabs for layout, annotations, and gene expression

Top region - Gene Knockouts

  • Search bar - find and add gene knockouts from the collection
  • Selected list - each row has an ⓘ (gene info) and a delete button
  • Counter in the top-right shows how many knockouts are selected

Bottom region - Layout, Annotations, and Gene Expression

  • Layout - add, remove, edit, and rearrange panels
  • Annotations - color all appropriate panels by a categorical annotation (e.g. cluster)
  • Gene Expression - color CROP-seq panels by a measured gene's expression level

Add Visualization sidebar showing three options with buttons for Embedding, Images, Volcano Plot

The book (📖) icon in the top-right of the left panel next to the collection name opens a Resources drop down with Documentation or Learn about OPS Explorer.

Three-dot overflow menu open showing Documentation and Learn about OPS Explorer

Visualization Panels

The right side of the viewer holds 1–4 visualization panes of four possible types:

Pane type Each dot is Used for
Embedding (UMAP-style) One gene knockout Cluster overview, perturbation grouping
Images (No dots - image grid) Browsing 3 channel cell crops per knockout x marker combination
OPS Feature Volcano One gene knockout Finding KOs with the largest morphological effect
CROP-seq Gene Expression Volcano One measured transcript (~20K dots) Finding differentially expressed genes for a chosen condition

Multi-panel view with all four panel types visible at once: OPS UMAP, OPS volcano, CROP-seq UMAP, CROP-seq gene expression volcano

Important: The CROP-seq Gene Expression Volcano is the only panel where dots are not gene knockouts. Annotation coloring and selection-from-list do not apply to it.

Essential Actions

Action What to do
Open a collection in the viewer Click Explore on the collection row
Select feature for OPS volcano Feature selector dropdown in top right of volcano panel
Find a knockout in the embedding Type the name in the Search for gene knockout(s) bar
See microscopy images for a KO With Images pane open in the viewer, select a gene knockout and the Images pane will populate automatically
Locate a knockout across all open panels Hover its name in the Gene Knockouts list, or its dot in any panel
Color all panels by cluster Annotations tab → click droplet icon (💧) button next to annotation category
Color CROP-seq panels by gene expression Gene Expression tab → add a gene → click its 💧 droplet icon
Open an image at full resolution Click any image → opens the idetik viewer in a new tab
Add a new panel Layout tab → + Add Visualization
Look up gene info Click ⓘ next to a KO name → Gene Info sidebar
See all KOs in a cluster Click ⓘ next to an annotation category in the Annotations tab → Cluster Info sidebar
View collection metadata Click ⓘ to the right of collection name at top of Layout panel
Download a collection Click ⤓ next to collection name → Download collection

Quick Tips and FAQ

Why is each dot a "gene knockout" and not a cell? Because the underlying data is aggregated per perturbation: each dot summarizes the average effect across all cells that received that knockout. UMAPs from CellxGene work differently (i.e., one dot = one cell).

Why doesn't annotation color appear on my CROP-seq Gene Expression Volcano? Dots in that panel are measured transcripts, not gene knockouts, so coloring by KO-level annotations doesn't apply. Coloring works on the other three panel types.

Why is the Gene Expression tab grayed out on my OPS panel? Per-gene expression data only exists for CROP-seq datasets. OPS panels show an amber ⚠ Limited badge when a gene expression overlay is active.

How do I tell which feature drives the OPS volcano? The feature selector dropdown is in the top-right of the volcano panel. The selected feature name also appears on the x-axis label.

How do I see images larger than the thumbnails? Click any image in the Images panel. It opens in the idetik viewer in a new browser tab for full-resolution viewing.

Can I undo a change to my panel layout or knockout selection? No, the viewer does not have undo/redo. Re-do the change manually.

Where are images coming from? Each gene knockout shows ~3 representative image crops per imaging marker, chosen by the dataset authors. The CONTROL row at the top is pinned at the top for visual comparison with the KO images. Viewers can access all images by downloading the entire collection.

How many panels can I open at once? Minimum 1, maximum 4. Layout orientation options change based on how many you have open.

Next Steps