Provide an observation-by-feature matrix and coordinates with matching observation IDs. Include feature names, source section labels and measurement units. H5AD, NPZ, CSV and TSV imports are supported.

• For H5AD, store coordinates in obsm["spatial"].
• For NPZ, include xyz, X, feature_names and sections.
• For tabular files, use one matrix and one coordinate table linked by ID.

Review the import checks before opening a 3D view. Confirm XY units, section order and physical Z spacing. A shared coordinate frame requires author registration or a documented alignment method.

• Use documented acquisition spacing. Display spacing is not instrument resolution.
• Keep independent specimens separate and retain original coordinate provenance.
• Unregistered sections can be inspected individually in the source browser.

In Analysis, select the dataset, task and method. Review the input summary and required annotations, then adjust the parameters for your sampling geometry and molecular modality.

• Use measured observations for tasks that require measured input.
• Distinguish training, parameter selection and held-out evaluation.
• Review an assistant-prepared configuration before submitting the job yourself.

Open a completed job to inspect its methods, parameters and outputs. In the viewer, compare molecular abundance with the source observations and examine linked virtual sections.

• Measured marks a source observation or an occupied source voxel.
• Predicted marks a model estimate at an unmeasured position.
• Author-resampled marks an interpolated or resampled author export.
• Review support masks, error units and validation scope before interpreting a pattern.