MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging

Highly multiplexed tissue imaging makes detailed molecular analysis of single cells possible in a preserved spatial context. However, reproducible analysis of large multichannel images poses a substantial computational challenge. Here, we describe a modular and open-source computational pipeline, MCMICRO, for performing the sequential steps needed to transform whole-slide images into single-cell data. We demonstrate the use of MCMICRO on tissue and tumor images acquired using multiple imaging platforms, thereby providing a solid foundation for the continued development of tissue imaging software.

Three-Dimensional Block Matching Using Orthonormal Tree-Structured Haar Transform for Multichannel Images

Multichannel images, i.e., images of the same object or scene taken in different spectral bands or with different imaging modalities/settings, are common in many applications. For example, multispectral images contain several wavelength bands and hence, have richer information than color images. Multichannel magnetic resonance imaging and multichannel computed tomography images are common in medical imaging diagnostics, and multimodal images are also routinely used in art investigation. All the methods for grayscale images can be applied to multichannel images by processing each channel/band separately. However, it requires vast computational time, especially for the task of searching for overlapping patches similar to a given query patch. To address this problem, we propose a three-dimensional orthonormal tree-structured Haar transform (3D-OTSHT) targeting fast full search equivalent for three-dimensional block matching in multichannel images. The use of a three-dimensional integral image significantly saves time to obtain the 3D-OTSHT coefficients. We demonstrate superior performance of the proposed block matching.