Nuclear and cellular foci detection using Fiji and QuPath

<p dir="ltr">Nuclear and cellular foci are ubiquitous in fluorescence microscopy images of cells and tissue (e.g. DNA damage response, protein aggregation, receptor clustering, vesicles, centromeres, FISH probes). <br><br>Foci Analyzer is a comprehensive user-friendly Fiji macro to detect, visualize and quantify foci in 2D and 3D fluorescence microscopy images of cells and tissue. Accurate cell/nuclei segmentation is achieved by utilizing StarDist and Cellpose. CLIJ2 and MorpholobJ are employed for efficient and reliable foci detection across different imaging modalities and resolutions. The output data include detailed foci statistics, segmentations overlay images and colocalization overlap maps. <br><br>We recently combined Foci Analyzer with QuPath, enabling foci analysis on very large images. Image tiles from annotated regions together with cell segmentations are exported from QuPath and analyzed in Fiji. <br>Foci results can be imported into QuPath, allowing cells to be classified on their foci characteristics. <br><br>Installation is straightforward via the Fiji Update Site 'Foci-Analyzer'. QuPath scripts are on GitHub. </p><p><br></p>