Node Index¶

This page lists all 108 operation specifications registered by NODE_LIBRARY in the current manual track. Nightly parameter behavior can be newer than the latest tagged alpha.

Scope of this reference

Titles and families were checked against the release registry. Input and output summaries describe the ordinary/default ports; Split Channels, Split Axis, Born-Wolf PSF, and other multi-output nodes can resolve ports from runtime data. Parameter widgets, defaults, and bounds in the installed release remain the source of truth until a generated parameter reference is published.

In 0.12.0a3, manual/cached nodes and nodes selected for isolated tuning use the same graph-wide execution language. Bright amber identifies the node that needs action; dark amber identifies downstream nodes that are stale but waiting for that action. Tune node in isolation recalculates only the selected node until the session is applied or cancelled. This changes execution and presentation, not the operation's scientific definition.

Family	Nodes
Image Data	24
Filtering	17
Segmentation	17
Morphology	13
Measurements	12
Colocalization & Spatial Analysis	10
Label Operations	7
Intensity & Contrast	5
Projection	3
Total	108

Image Data¶

Source And Output¶

Node	Input	Output	Use
`Image Source`	none	image	Load a napari layer, file, store, or bundled sample.
`Save Image`	array	any	Save an image-like output during interactive recompute.
`Batch Output`	any	same as input	Mark an output for folder batch execution.

Axes And Regions¶

Node	Input	Output	Use
`Crop Stack`	array	image	Crop spatial edges.
`Select Axis Slice`	array	any	Keep or select an index/range along an axis.
`Split Axis`	array	dynamic outputs	Split time, z, or other non-channel axes.
`Reorder Axes`	array	same as input	Reinterpret and transpose axis order.
`Set Pixel Size / Units`	array	same as input	Repair or define physical calibration.
`Rescale Axes`	array	same as input	Resample X/Y/Z and update physical scale.

Channels And Composites¶

Node	Input	Output	Use
`Extract Channel`	array	image	Select one channel from a multichannel image.
`Combine Channels`	array inputs	image	Stack inputs into a multichannel image.
`Split Channels`	array	dynamic outputs	Emit one output per channel.
`Composite → RGB`	array	image	Render multichannel data as RGB.
`Assign Channel Colors`	array	same as input	Change carried channel display colors.

Composite → RGB separates Channel axis mode and RGB mapping mode. Each can be Auto, with its resolved choice shown read-only, or Manual. Manual axis mode permits any valid deliberate axis choice. Manual mapping provides a dynamic selector for every source channel: Unassigned, Red, Green, Blue, Magenta, Cyan, or Yellow. Unassigned channels contribute nothing; all assigned channels, including stacks wider than RGB/RGBA, mix additively. Changing the mapping invalidates the composite and its descendants only. Every calculated manual result upstream remains cached in every cache mode; unchanged automatic intermediates remain eligible for normal Smart/Low-memory pruning. Intensity mapping is a separate native-preserving versus explicitly lossy percentile choice.

Math And Logic¶

Node	Input	Output	Use
`Calculate New Image`	arrays	image	Weighted multi-input image calculation.
`Add`	arrays	image	Add images.
`Subtract`	arrays	image	Subtract images.
`Ratio`	arrays	image	Ratio image with epsilon guard.
`Mask Image`	image plus mask/labels	image	Apply mask to image, broadcasting over compatible axes.
`Logical AND`	arrays	mask	Combine masks.
`Logical OR`	arrays	mask	Combine masks.
`Logical XOR`	arrays	mask	Exclusive mask combination.
`Invert`	any	any	Invert masks or intensity-like inputs.

Utilities¶

Node	Input	Output	Use
`Convert Dtype`	array	any	Convert array dtype.

Intensity And Contrast¶

Node	Output	Use
`Linear Scale + Offset`	image	Apply scale and offset.
`Gamma Correction`	image	Nonlinear brightness/contrast remapping.
`Rescale Intensity`	image	Contrast stretch between input/output ranges.
`Normalize`	image	Normalize intensity values.
`Clip`	image	Clip intensity range.

Rescale Intensity offers exact full-input percentiles or saved explicit input values. Clip offers an unchanged full-data-range mode or saved explicit clamp values. Integer percentiles and clipping preserve native int64/uint64 levels; unrepresentable fractional bounds or intervals too wide for faithful ratio arithmetic report an error rather than being silently rounded. Auto Contrast for Linear Scale + Offset writes calculated parameters and is not merely a display adjustment. See Tune without fooling yourself.

Filtering¶

Background Correction¶

Node	Output	Use
`Rolling-Ball Background`	image	Estimate background.
`Subtract Background`	image	Remove smooth background.

Smoothing And Denoising¶

Node	Output	Use
`Average Blur`	image	Simple local averaging.
`Gaussian Blur`	image	Gaussian smoothing.
`Gaussian Blur 3D`	image	Volumetric Gaussian smoothing.
`Median Filter`	image	Remove salt-and-pepper noise.
`Bilateral Filtering`	image	Edge-preserving smoothing.
`Non-Local Means`	image	Denoising for suitable data.

Edge And Detail¶

Node	Output	Use
`Difference of Gaussians`	image	Enhance features by scale difference.
`Unsharp Mask`	image	Sharpen details.
`Sobel Edges`	image	Edge magnitude image.
`Canny Edges`	mask	Edge mask.
`Laplace Filter`	image	Laplacian edge/detail response.

Restoration And PSF¶

These nodes are public in 0.12.0a3. They have synthetic examples and automated coverage, but broad real-image restoration validation remains an evidence gap; see validation status.

Node	Input	Output	Execution	Use
`Born-Wolf PSF`	image/reference metadata	image	automatic	Generate a PSF from metadata or parameter overrides.
`Prepare / Validate PSF`	image	image	automatic	Center, clip, normalize, and validate a PSF.
`Richardson-Lucy Deconvolution`	image plus PSF	image	manual	Baseline PSF-aware deconvolution.
`Richardson-Lucy TV Deconvolution`	image plus PSF	image	manual	TV-regularized Richardson-Lucy restoration.

Projection¶

Node	Output	Use
`Maximum Projection`	image	Quick maximum intensity projection.
`Project Image`	image	Axis-aware projection with selectable reducer.
`Orthogonal Projection`	image	Orthogonal view respecting physical scale.

Segmentation¶

Global Thresholds¶

Node	Output
`Otsu Threshold`	mask
`Triangle Threshold`	mask
`Li Threshold`	mask
`Yen Threshold`	mask
`Isodata Threshold`	mask
`Minimum Threshold`	mask
`Binary Threshold`	mask
`Hysteresis Threshold`	mask

Otsu, Triangle, Yen, Isodata, and Minimum count every finite input value. Integers use exact native levels for observed spans up to 65,536; floats use the saved 2–65,536 bin setting (default 256). Li operates on raw finite values. Minimum also saves its maximum smoothing iterations and fails explicitly when it cannot identify a valid two-peak histogram. See Segmentation and label cleanup.

Local Thresholds¶

Node	Output
`Adaptive Mean Threshold`	mask
`Adaptive Gaussian Threshold`	mask
`Sauvola Threshold`	mask
`Niblack Threshold`	mask

Object Separation¶

Node	Input	Output	Use
`Auto Watershed From Mask`	mask/array	labels	One-node marker watershed helper.
`Euclidean Distance Transform`	array	image	Distance map for watershed.
`H-Maxima Markers`	array	labels	Marker generation.
`Marker-Controlled Watershed`	image/distance plus markers plus mask	labels	Split touching objects.
`Expand Labels`	labels	labels	Grow labels without overlap.

Morphology¶

Node	Input	Output	Use
`Dilation`	array	mask	Expand foreground.
`Erosion`	array	mask	Shrink foreground.
`Opening`	array	mask	Remove small foreground structures.
`Closing`	array	mask	Close small gaps.
`Top Hat`	array	mask	Binary top-hat operation.
`Black Hat`	array	mask	Binary black-hat operation.
`Morphological Gradient`	array	mask	Boundary-like morphology response.
`Fill Holes`	mask	mask	Fill enclosed holes by area/volume.
`Remove Small Objects`	mask or labels	same type	Remove connected objects below size threshold.

Skeleton / Network QC¶

Node	Input	Output
`Skeletonize`	mask	mask
`Skeleton Keypoints`	mask	endpoints, junctions, isolated masks
`Skeleton Graph Overlay`	mask	RGB image
`Prune Skeleton Branches`	mask	mask

Label Operations¶

Node	Input	Output	Use
`Label Connected Components`	mask	labels	Convert mask to object IDs.
`Clear Border Objects`	mask or labels	same type	Remove objects touching image boundary.
`Filter Labels By Volume`	labels	labels	Keep/remove labels by pixel/voxel count.
`Filter Labels By Property`	labels plus table	labels	Filter labels using table columns.
`Relabel Sequential`	labels	labels	Compact labels after filtering.
`Label Skeleton Components`	mask	labels	Label connected skeleton components.
`Label Skeleton Branches`	mask	labels	Label skeleton branch paths.

Measurements¶

Node	Input	Output	Execution	Use
`Measure Objects`	labels	table	manual	Object morphology.
`Measure Objects + Intensity`	labels plus intensity image	table	manual	Object morphology plus intensity statistics.
`Measure 3D Mesh Morphology`	labels	table	manual	Surface/mesh morphology for true 3D labels.

Skeleton / Network QC¶

Node	Output	Execution
`Analyze Skeleton`	table	manual
`Measure Skeleton Branches`	table	manual
`Summarize Skeleton Branches`	table	automatic
`Skeleton Graph Tables`	graph-node table and graph-edge table	manual
`Measure Overall Skeleton Network`	table	manual

Tables¶

Node	Input	Output	Use
`Merge Tables`	tables	table	Join measurement branches.
`Add Metadata Columns`	table	table	Add treatment, replicate, condition, batch, or other fields.
`Select Table Columns`	table	table	Keep and reorder columns.
`Summarize Measurements`	table	table	Group rows and calculate summary statistics.

Colocalization And Spatial Analysis¶

Node	Input	Output	Execution
`Colocalization Metrics`	channel 1 plus channel 2	table	manual
`Masked Colocalization Metrics`	channel 1 plus channel 2 plus ROI	table	manual
`Colocalized Voxels`	channel 1 plus channel 2	image	automatic
`Masked Colocalized Voxels`	channel 1 plus channel 2 plus ROI	image	automatic
`RACC Index`	channel 1 plus channel 2	image	manual
`Masked RACC Index`	channel 1 plus channel 2 plus ROI	image	manual
`Object Colocalization Metrics`	labels plus two channels	table	manual
`Label Overlap Association`	reference plus target labels	table	manual
`Nearest Object Distance`	reference plus target labels	table	manual
`Event Localization`	events plus regions	table	manual