Reference: every SP Classify menu item

All under Extensions → SP Classify, in menu order.

Item	Requires	Action
Binary Classifiers...	Project	Opens the binary classifier manager: create, open or delete one classifier per marker.
Composite Classification...	Project + ≥1 trained binary classifier	Applies trained binary classifiers and assigns composite labels.
Class Control...	Project	Add, delete, merge and undo-merge classes.
Channel Mapping (Review Display)...	Open image	Sets which image channels review shows for each class. Saved per project, with CSV import and export. See Marker table format.
Select Features...	Project	Choose which measurement columns are used for training.
Clustering Normalisation	Project	Sets an arcsinh or square-root transform per feature, with a shared cofactor, for clustering only. The classifier uses raw values. See §4.2.
Project Prediction Summary...	Project	Cohort QC: anomaly score and flags for each image. See §8.
Intensity Heatmaps...	Open image with detections	Heatmap of mean marker intensity per class (z-score colours), for one image or the whole project. PNG and CSV export. See §9.
Image Pixel Prescreen...	Project	Whole-image QC without cells: per-channel pixel statistics compared across the project, with flags for background-heavy, saturated, weak-signal and intensity-outlier images. CSV export. See §17.
Scatter Plots and Clustering...	Open image with detections	PCA/UMAP scatter plot with k-means or Leiden clustering, annotation and class gating, and cluster → class assignment. Scope switches to clustering across several images. See §11.
Cellular Neighborhoods...	Open image with cells in at least 2 classes	Groups cells by the cell types around them (k-means on neighbourhood composition), for one image or the whole project. See §18.
Batch Normalisation...	Project	Aligns each marker's intensity across images (UniFORM). Fit and QC, then use the corrected values in clustering and the classifier, or write them as (batchnorm) columns. See §19.
Generate Distance Measurements...	Project	Distances to annotations (signed), to other classes, and to the nearest cell of the same class, for the selected images. See §10.
Export → Cell Table...	Open image with detections	One CSV per selected image. See §12.1.
Export → Ground Truth...	Open image with labels (multi-class)	CSV of labels and feature values that you can import into another project.
Export → Active Binary Ground Truth...	Binary mode active + open image with labels	As above, for the active marker only.
Import → Marker Table...	Open image	Loads a cell type → markers CSV used to switch channels during review. The Channel Mapping editor is the recommended way to edit it.
Import → Ground Truth...	Open image (multi-class)	Imports labels by spatial match, or as training data only.
Import → Active Binary Ground Truth...	Binary mode active + open image	As above, for the active marker only.
Utility Scripts → Filter Cells by Size & Circularity...	Open image with cells	Removes cells outside optional area and circularity limits, in the current image. See §13.1.
Utility Scripts → Resolve Hierarchy...	Open image or project	Rebuilds parent/child relationships between objects, for the current image or the whole project. See §13.2.
Utility Scripts → Lock All Annotations	Open image or project	Locks every annotation, in the current image or in all project images, so it cannot be moved or edited by accident. See §13.7.
Utility Scripts → [TEST] Import GeoJSON Objects...	Open image	Imports objects from a GeoJSON or gzipped GeoJSON file into the current image. Small to medium files only. See §13.4.
Utility Scripts → [TEST] Export Annotation Regions...	Open image	Exports annotation regions from the current image as polygon-masked OME-TIFF files. One image, small to medium regions only. See §13.5.
Utility Scripts → Delete Measurements by Keyword...	Open image or project	Destructive: deletes detection measurements whose names contain a keyword. Shows the matches and asks you to confirm. See §13.3.
Utility Scripts → Reset Project State...	Project	Destructive: deletes the project's celltune/ folder (labels, models, predictions, settings). Writes a backup zip first and asks you to type RESET. Can also clear SP Classify label points and cell classifications from every image. See §13.6.
How to Cite...	Nothing (always available)	Shows the references to cite for SP Classify and for the methods you used.

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