A neural atlas explorer

Find the evidence behind a spatial result.

NeuroViz brings datasets, atlas context, and provenance into one readable research surface—so every view can be examined, understood, and revisited.

Browse the Allen MERFISH dataset

Animated Allen MERFISH brain mesh with spatial cells, rotating and moving closer to the selected view. — Allen MERFISH · a 360° orbit through the atlas, with a closer view into the spatial cells.

Allen MERFISH-C57BL6J-638850

A spatial cell atlas built for questions that start with place.

The release contains 4.3 million QC-passed cells from one adult mouse brain, profiled with a 500-gene MERFISH panel across 59 coronal sections. Each cell can be considered in its anatomical, taxonomic, and registered spatial context.

In the explorer

Move from a broad atlas to an inspectable cell cohort.

Allen MERFISH explorer showing anatomical and cell-type filters

01 · Define a cohort

Filter cells without losing the anatomical question.

Start with an anatomical region, then refine the cohort by provider class or subclass. Gene-expression range, section, layer, and quality controls let you make the inclusion criteria explicit before interpreting a spatial pattern.

Open the Allen MERFISH filters

Allen MERFISH explorer showing matching cell records

02 · Inspect the result set

Keep the cell data visible while you work.

The explorer reports both the displayed sample and the full matching count. Open the cell records to sort the current cohort and move from an aggregate spatial pattern to individual cell-level metadata, taxonomy, and measured expression.

View matching cell records

Allen MERFISH explorer showing the three-dimensional brain and camera controls

03 · Read the spatial context

Navigate the brain without leaving the cell view.

Rotate, zoom, pan, and reset the 3D camera to examine the selected cohort from a useful angle. Separate mesh and cell controls help reveal the spatial distribution while retaining the anatomical reference frame.

Explore the 3D cell view

Selected Allen MERFISH cell with its matching-record row and measured-expression inspector

04 · Inspect an individual cell

Turn a selected cell into a reviewable observation.

Select a point in the brain or a row in the matching-cell table to open the cell inspector. Review its anatomical assignment, provider taxonomy, source section, and measured expression values without losing the cohort that led you there.

Open the cell inspector

Research use cases

Start with a research question, not a visualization.

Explore cell identity and measured expression within 3D anatomy. These illustrative workflows make clear what the current explorer can support and where a proposed, validated extension is needed.

View all research use cases