Utility scripts¶

Extensions → SP Classify → Utility Scripts

Tools for common cleanup tasks. Each one asks for its settings, then reports what it changed.

13.1 Filter Cells by Size & Circularity¶

Removes cell detections from the current image that fall outside size and shape limits. The dialog has a row for Area and a row for Circularity (0–1). Each row has a Measurement dropdown and Min and Max boxes. The dropdowns list every measurement whose name contains "area" or "circularity" and start on the whole-cell measurement (Cell: Area µm^2, or Cell: Area px^2 if the image is not calibrated, and Cell: Circularity). Change them to filter on, for example, nucleus area. Area limits are in the units of the chosen measurement. The dialog opens with Max area = 500 and Min circularity = 0.7. Clear a box to remove that limit. A cell is removed if it breaks any limit (e.g. Cell: Area µm^2 > 500 or Cell: Circularity < 0.7). Cells missing a measurement that has a limit are kept. The number of cells to be removed is shown before anything is deleted.

13.2 Resolve Hierarchy¶

Rebuilds parent/child relationships from object outlines, the same as the resolveHierarchy() script command. Choose Current image (applied immediately) or All project images (asks to confirm, then resolves and saves every image). The open image updates immediately; other images are processed in the background.

13.3 Delete Measurements by Keyword¶

⚠️ Destructive and cannot be undone. Check the keyword against your measurement names. A short keyword can match more columns than you intend.

Removes every detection measurement whose name contains a keyword. Matching ignores case unless you tick Case sensitive. Choose Current image or All project images. Before deleting, the extension lists the matching columns and asks you to confirm. If nothing matches, nothing is deleted. With All project images, every image is saved (the open image first, the rest in the background).

13.4 Import GeoJSON Objects¶

⚠️ For small-to-medium GeoJSON files only. This importer loads the whole file into QuPath's memory. Very large files (hundreds of MB or millions of objects) can run out of memory and crash QuPath. For those, use the headless pipeline: github.com/BioimageAnalysisCoreWEHI/import_large_geojson.

Menu: Utility Scripts → [TEST] Import GeoJSON Objects...

Imports annotations and detections from a .geojson or .geojson.gz file into the current image. Options (both off by default): Clear existing objects first, and Resolve hierarchy after import. The second can take a long time with many objects. Annotations are added and locked first, then detections, and the image is saved.

13.5 Export Annotation Regions¶

⚠️ Single image, small-to-medium regions. For very large regions or exports from a whole project, the headless pipeline on HPC is much faster: github.com/BioimageAnalysisCoreWEHI/export_large_annotation_regions.

Menu: Utility Scripts → [TEST] Export Annotation Regions...

Exports annotations from the current image as OME-TIFFs. Pixels outside each annotation's outline are set to 0. Enter annotation names separated by commas, or leave blank to export all annotations. Defaults: Downsample 1.0, Tile size (px) 512, Writer threads = number of CPU cores (maximum 32), Compression LZW, BigTIFF on, Build pyramid on. Each region is saved as <image>__<annotation>.ome.tif in the folder you choose, and a notification reports how many succeeded. Requires QuPath's Bio-Formats extension (included and loaded by default).

13.6 Reset Project State¶

⚠️ Destructive. Deletes everything the extension has saved for this project. Use it to start again, e.g. after copying a project to try different classifier settings: the celltune/ folder is copied with the project.

Deletes the project's celltune/ folder: all labels and per-image label files, trained classifiers (multi-class and binary) and predictions, feature selection, normalisation, marker table, composite rules, and sampling/review state. It also resets the current session so the old state is not saved again.

Backup: before deleting, the extension writes celltune_backup_<timestamp>.zip to the project folder. To undo the reset, unzip it into the project folder. This recreates celltune/. To confirm the reset, type RESET.

Images and detections are kept. The extension's ground-truth label points and the cell classifications (predictions) are stored in each image's .qpdata, not in celltune/, and are kept by default. To remove them too, tick "Also clear SP Classify label points and all cell classifications from every image". This deletes classified point annotations and clears every cell's classification in all project images, and saves each image. Tissue/region annotations and unclassified points are never changed.

13.7 Lock All Annotations¶

Locks every annotation so it cannot be moved or edited by mistake. Choose Current image or All project images (asks to confirm, then saves every image). A notification reports how many annotations were locked.