Software solutions for CyCIF and beyond

We develop opensource software to tackle common challenges imposed by the highly-multiplexed whole slide imaging.


Minerva is a suite of software tools for interpreting and interacting with complex images, organized around a guided analysis approach. The software enables fast sharing of large image data that is stored on Amazon S3 and viewed using a zoomable image viewer implemented using OpenSeadragon, making it ideal for integration into multi-omic browsers for data dissemination of tissue atlases. Check out the Minerva Wiki to learn more about the software and for news.

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ASHLAR (Alignment by Simultaneous Harmonization of Layer/Adjacency Registration) is Python tool for image registration and stitching that is more rapid and accurate than existing methods in assembling subcellular-resolution, multi-channel images up to several square centimeters in size. ASHLAR uses Bioformats software to read virtually any microscope image files and write the OME-TIFF format files.

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MCMICRO is the end-to-end processing pipeline for multiplexed whole tissue imaging and tissue microarrays. It comprises stitching and registration, segmentation, and single-cell feature extraction. Each step of the pipeline is containerized to enable portable deployment across an array of compute environments, including local machines, job-scheduling clusters and cloud environments like AWS. The pipeline execution is implemented in Nextflow, a workflow language that facilitates caching of partial results, dynamic restarts, extensive logging and resource usage reports.

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