Synapse Formation Embeddings Browser

The viewer presents data from the synapse formation cell dataset referenced in the following paper:
PXPermute reveals staining importance in multichannel imaging flow cytometry, Shetab Boushehri, Sayedali et al. Cell Reports Methods, Volume 4, Issue 2, 100715

Usage

Detaset Map

The Dataset Map section displays a~plot of 2D-reduced embeddings of your dataset. The map is zoomable and draggable - you can easily zoom in onto parts of the plot. Hovering over points in the plot displays detailed information on individual samples.

Map options

The paragraph above the Map lets you choose how the points in the plot are colored (color by) and which points are highlighted (filter by). Below the Map there are controls that allow you to change the point size, and select channels that are displayed in cell previews.

Selected cell and its neighbors

Clicking on a point in the Map selects the corresponding cell and makes it appear in the Selected cell and its neighbors section. Below the cell there are previews of 25 cells that have most similar embeddings. You can hover over the cells to view their metadata, or click on them to select them.

Selection of random cells in visible Map area

After clicking Pick random cells, this section provides a preview of randomly chosen cells which are highlighted (if a filter is chosen) and are currently visible in the Map. This way, you can zoom in to specific section of the Map and browse a random selection of cells from this area.