Use your own images

An Image Source can read a napari layer, a local file or store, or a bundled sample. Changing the source is easy; establishing that the workflow remains valid is the important part.

Choose a source route

Route	Best for	Important limitation
napari layer	Images already opened, cropped, or registered in napari	The workflow depends on a layer being present and correctly selected; unsupported live/lazy transforms can be rejected.
file path	A repeatable local file input	Moving, renaming, or replacing the file changes/breaks the source identity.
sample	Tutorials, regression checks, and demonstrations	Synthetic data does not establish performance on your assay.
Local OME-Zarr store	Chunked multidimensional data	Many operations are eager and can still materialize large arrays.

Select Image Source, set Source, and then use the control specific to that route. The napari layer chooser is only shown for napari layer.

Understand the source revision

During one interactive revision, VIPP does not repeatedly read an uncontrolled moving target. A local file or directory store is identified before and after inspection/materialization, detached into an owned read-only snapshot, and pinned until Refresh. A revision changed during calculation is rejected.

NumPy-backed napari layers are also copied with a revision token. Data, metadata, RGB, axis, scale, translation, unit, rotation, shear, and affine events invalidate stale work. VIPP rejects live data or transforms that cannot be frozen without changing pixels.

Refresh is the explicit instruction to accept the current source revision. Record an external checksum or repository identifier for long-term provenance; the workflow stores a source parameter/path, not the image bytes.

Check metadata before processing

Confirm at minimum:

• array shape and semantic axes (T, C, Z, Y, X);
• channel order and names;
• pixel size, z-step, and unit;
• whether the data is intensity, RGB, a binary mask, or labels;
• whether the reader selected the intended image/series.

For a multi-input node, also confirm that corresponding axes describe the same physical grid. Equal shape does not prove equal scale, units, origin, or axis meaning. VIPP rejects detected mismatches rather than resampling silently.

Use Reorder Axes only when you understand the actual stored order. Use Set Pixel Size / Units to repair missing or known-wrong calibration, and record where the corrected values came from.

Transfer a workflow deliberately

Do not judge transfer only from the final object count. On representative images from the new acquisition family:

1. Inspect raw channel quality and background.
2. Inspect every threshold or segmentation boundary.
3. Check objects at image edges and across z.
4. Compare against independent reference annotations or agreed QC examples.
5. Retune only on a defined tuning subset.
6. Evaluate the frozen workflow on held-out images.

Changes in objective, exposure, stain, detector, bit depth, sampling, tissue, or preprocessing can invalidate parameters that worked previously.

When moving a schema-1/2 workflow to 0.12, rebuild it deliberately and resolve new explicit channel-axis, RGB/intensity mapping, and grid choices. See versions and compatibility.

Protect sensitive data

Workflow JSON may contain local paths, source names, graph notes, or metadata values. Review it before sharing publicly. Do not use patient identifiers, restricted paths, or unpublished biological conclusions in screenshots, examples, notes, or metadata columns.

Continue to segmentation, measurements, or the scientific-practice checklist.