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Welcome to the StereoMate wiki!

StereoMate is a suite of ImageJ plugins designed to perform automated stereological analysis on confocal image stacks.

The StereoMate pipeline:

• Develops image segmentation protocols with rigorous validation

• Extracts an object-level multivariate dataset in an automated and stereological manner.

For a whistle-stop tour see Quick start, otherwise navigate the documentation in the panel to the left.

The software is freely available for download in FIJI/ImageJ comprises a common file structure for the batch processing of image stacks through the StereoMate pipeline.

The StereoMate pipeline consists of:

1. Confocal image stack deconvolution with built-in PSFs (StereoMate Deconvolution).
2. Delineation of Regions of Interest (StereoMate ROI Manager).
3. Development of image segmentation protocols (StereoMate Threshold Manager).
4. Processing of segmented objects (StereoMate Object Manager).
5. Assessment of segmented objects by ROI, using a novel stereological filter (StereoMate Analyser).