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A software package that combines multi-tile microscopy images into a high-dimensional mosaic image.

OVERVIEW Quick Start

Key Features

Precise stitching for single-cell level accuracy

ASHLAR uses a novel alignment method that results in improved accuracy across imaging cycles.
The first cycle of images are combined by aligning and stitching overlapping regions, then images between cycles are aligned by finding the relative position of images from each subsequent cycle to the first cycle image. This minimizes alignment errors between cycles.

Designed for multiplexed images

ASHLAR has been optimized for computationally-efficient generation of high dimensional mosaic images.

Supports irregular sample geometries

ASHLAR allows reconstruction of irregular and discontinuous sample edges, as is often seen in biological slide samples.

Seamlessly compatibile with standard microscopy workflows

ASHLAR directly reads image formats that are compatible with most commercial microscopes and slide scanners, and it outputs standard OME-TIFF images.

Open source

ASHLAR is written in Python and is available under the MIT License. It can be downloaded at:

Integrated into the Multiple Choice Microscopy Pipeline

For more information about the MCMICRO pipeline for processing multi-channel images into single cell data, see

For more details, read the manuscript in Bioinformatics:

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