TY - JOUR T1 - QuickStitch for seamless stitching of confocal mosaics through high-pass filtering and recursive normalization JF - bioRxiv DO - 10.1101/075440 SP - 075440 AU - Pavel A. Brodskiy AU - Paulina M. Eberts AU - Cody Narciso AU - Jochen Kursawe AU - Alexander Fletcher AU - Jeremiah J. Zartman Y1 - 2016/01/01 UR - http://biorxiv.org/content/early/2016/10/24/075440.abstract N2 - Fluorescence micrographs naturally exhibit darkening around their edges (vignetting), which makes seamless stitching challenging. If vignetting is not corrected for, a stitched image will have visible seams where the individual images (tiles) overlap, introducing a systematic error into any quantitative analysis of the image. Although multiple vignetting correction methods exist, there remains no open-source tool that robustly handles large 2D immunofluorescence-based mosaic images. Here, we develop and validate QuickStitch, a tool that applies a recursive normalization algorithm to stitch large-scale immunofluorescence-based mosaics without incurring vignetting seams. We demonstrate how the tool works successfully for tissues of differing size, morphology, and fluorescence intensity. QuickStitch requires no specific information about the imaging system. It is provided as an open-source tool that is both user friendly and extensible, allowing straightforward incorporation into existing image processing pipelines. This enables studies that require accurate segmentation and analysis of high-resolution datasets when parameters of interest include both cellular-level phenomena and larger tissue-level regions of interest. ER -