PointillViz docs

From your first import to your first figure.

Eleven tutorials, in the order you will need them. They are in preparation, and each page already lists what it will cover.

Start here

New to PointillViz? Bring in one section, explore it, export a figure.

Importing
An .h5ad to the viewer, in three steps.
2D data
Colours, the Lens, regions and gates.
Exporting
Figures at up to 8×, results as CSV.

A Xenium 5K mouse colon section, rolled into a spiral: every cell drawn as a point in its cell-type colour. — 2D · SectionXenium 5K · mouse colon · 135,232 cells

Start

Bring your data in.

The import wizard at its Map fields step: the Spatial panel set to 2D spatial, with the spatial obsm key and pixel units, and the Cells panel with a cell-type column of 73 types, an automatic palette and the hierarchy options.

Importing

Bring an .h5ad into PointillViz: the import wizard maps its fields onto the viewer and converts it.

Outline

Xenium 5K · mouse colon · 135,232 cells5 topics

Data

Sections, volumes, atlases and modalities.

The Lens over a mouse colon section coloured by cell type: its loupe on the mucosa, and the Under the lens panel listing the cell types in view and in the loupe.

2D · Section

2D data

Explore one tissue section: colour it by type or gene, read the Lens, draw regions and gate cells.

Xenium 5K · mouse colon · 135,232 cells6 topics

A HER2⁺ breast carcinoma imaged by 3D imaging mass cytometry, drawn as a volume of cells coloured by HER2, with the Scale and orientation panel and its X, Y and Z bars.

3D · Volume

3D data

Orbit a volume, cut it into slabs and select the cells inside them.

3D imaging mass cytometry · HER2⁺ breast carcinoma · 108,486 cells5 topics

A 39-section mouse colon atlas composed into one montage, coloured by cell type.

Atlas · Cohort

Atlases

Compose harmonized sections into one live montage, and compare conditions over every cell of the cohort.

Mouse colon · 39 sections · 11,443,143 cells6 topics

Pde10a in RNA, ATAC, H3K27ac and H3K27me3, four maps of the same mouse brain section side by side.

Multi-omics

Multimodal

Compare RNA, chromatin accessibility, histone marks and protein measured on the same spots.

Spatial-Mux-seq · mouse brain · 9,686 spots6 topics

Layers

Images, outlines and molecules with the cells.

Images

Lay H&E and multiplexed stains under the cells, and set each channel’s colour and levels.

Xenium 5K · mouse colon · H&E6 topics

Polygons

Draw cells as their segmentation outlines, from the whole section down to a single cell.

Xenium 5K · mouse colon5 topics

Molecules of Epcam, Acta2 and Lyz1 as green, pink and cyan glowing spots over the greyed cells of a Xenium 5K mouse tissue microarray.

Transcripts

Draw every detected molecule over the cells, and replay sequencing depth from 1% to 100%.

Xenium 5K · mouse tissue microarray5 topics

Results

Figures and tables to take with you.

A captured view of cells coloured by type, with the cell-type legend beside it.

Exporting

Save views as PNG, PDF or SVG figures at up to 8×, and computed results as CSV files.

Outline

Xenium 5K · mouse colon6 topics

Extend

Community tools and the AI assistant.

Tool Store

Install community tools, run them like built-in analyses, and publish your own.

Browse the Tool Store Build & publish

12 tools · 9 gates6 topics

The Assistant panel beside a Spatial-Mux-seq mouse brain section coloured by cluster: its first notebook result, R01, a figure of chromatin signal against expression across RNA clusters, with its derivation script listed below.

AI assistant

Ask in plain language: a coding agent reads your data, runs tools and publishes results to a notebook.

Spatial-Mux-seq · mouse brain · 9,686 spots6 topics