Visualizing and sharing CyCIF images

For a ~10 x 11mm tissue FFPE specimen under 20X objective, each cycle of t-CyCIF generates around 160 individual image tiles. The assembly process involves stitching sequential image tiles from a single t-CyCIF cycle into one large image panel, flat-fielding to correct for uneven illumination and registration of images from successive t-CyCIF cycles to each other; these procedures were performed using ImageJ, ASHLAR, and BaSiC software.

The stitched images are stored on Amazon S3 and the zoomable image viewer implemented using OpenSeaDragon.

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Tour of the melanoma dataset

The unpublished 13-plex t-CyCIF images of tissue specimens from four patients with BRAF-mutant metastatic melanoma resected before (left) and after (right) treatment with BRAF and MEK inhibitors (dabrafenib/trametinib). Each image is composed of 150-200 image tiles at a nominal resolution of ~0.9 μm.

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Figures in the 2018 eLife Publication

Tissue-based cyclic immunofluorescent microscopy (t-CyCIF) is a simple method for generating highly multiplexed optical images from formalin-fixed paraffin-embedded (FFPE) tissue samples routinely used for histopathological diagnosis of human disease. The method is based on previously described single-cell imaging approaches and readily implemented on existing instruments (Gerdes et al. 2013, Lin et al. 2015, 2016).