Scope2Screen
Scope2Screen is an extension for 'minerva_analysis' to allow focus+context based exploration of image channels and linked single cell data.
The extension offers (A) Channel & color selection for multi-channel rendering. (B) A WebGL-based viewer capable of rendering 100+GB sized high-plexed and high-resolution (≥30k×30k) image data in real-time. (C) Interactive lensing forclose-up analysis - the lens shows a multi-channel immune setting that is different from the global context highlighting basic tissue composition. (D) Dotter panel - stores and organizes snapshots of annotated ROIs to filter, restore, navigate to the image location.
The code is available in our seperate scope2screen repository:
- Scope2Screen: https://github.com/labsyspharm/scope2screen
This branch integrates our standalone WIP branch for 'minerva_anaysis' that implements and customizes lens tooling as an OpenSeaDragon pluging.
- Lensing github: https://github.com/jessupjs/lensing
- Lensing npm: https://www.npmjs.com/package/lensing
- Lensing standalone demo: https://the.andwonders.works/vcg/lensing-demo/
Download latest release and execute it. This will start a local server on your machine. Open the browser and navigate to: http://mts-lsp-l06208:8000/
- Clone locally from Github:
git clone -b lensing git@github.com:labsyspharm/minerva_analysis.git- or, switch to branch:
git switch lensing
- or, switch to branch:
- Run from readme.md (no new env updates)
Different settings can be used to magnify the lens area.
To magnify press "." to zoom out press ",". To switch the magifier press "m".
Standard | Fisheye | Plateau
The lens shape can be changed by pressing "⇧ l".
The lens offers different image filters. To switch the feature press: Previous lens: "⇧ [" // Next lens: "⇧ ]"
Generic: Grayscale | Invert | Threshold | Gamma | Context-adaptive: Sobel Edge
The lens offers different image channel filters. To switch the feature press: Previous lens: "⇧ [" // Next lens: "⇧ ]"
Generic: Single Channel| Multi-Channel | Splitscreen
The lens offers different single-cell features, linking extracted single-cell statistics with the image space. To switch the feature press: Previous lens: "⇧ [" // Next lens: "⇧ ]"
Data-driven: Segmentation Mask | Cell Types | Single Cell istribution - Histograms | Single Cell Means - Radial
For a region of innterest (ROI) a snapshots can be taken by pressing "⇧ d". The taken snapshot then appears in the Dotter panel on the right side of the tool.
The rich snapshot and annotation process. (A) During close-up analysis, the user focuses on an ROI and takes a snapshot. (B) The snapshot is annotated with title and description and saved to a database. (C) The Dotter panel links snapshots to the image space (left). Lens-settings such as channel combination and colors are preserved. (D) Annotated regions can be reactivated as lenses to explore further or fine-tune.
The lensing features are currently steered via keys (we are working on a user interface/button). Here is a Cheat Sheet (click for pdf) for all possible features:
Reduce: [
Increase: ]
Zoom In: .
Zoom Out: ,
No zoom: /
Ruler: ;
Default: \
Previous lens: ⇧ [ , {
Next lens: ⇧ ] , }
None: ⇧ \ , |
Put-down/pick-up: p
Snapshot: ⇧ d, D
Lens Shape: ⇧ l, L
Toggle visible/hidden: l
Toggle magnification modes: m
Histosearch lens: increase sensitivity with k/reduce with j, trigger search with h, delete current selection with x.