WormSNAP: A software for fast, accurate, and unbiased detection of fluorescent puncta in C. elegans

The detection and characterization of fluorescent puncta are critical tasks in image analysis pipelines for fluorescence imaging. Existing methods for quantitative characterization of such puncta often suffer from biases and limitations, compromising the reliability and reproducibility of results. Moreover, the widespread adoption of many available analysis scripts is often hampered by over-optimization for specific samples, requiring extensive coding knowledge to repurpose for other datasets. We present WormSNAP (Worm SyNapse Analysis Program), a freely available, stand-alone, no-code approach to automated unbiased detection and characterization of 2D fluorescent puncta, originally developed to characterize images of the synapses residing in C. elegans nerve cords but suitable for broader 2D fluorescence image analysis. WormSNAP incorporates a local means thresholding algorithm and a user-friendly Graphical User Interface (GUI) for efficient and accurate analysis of large datasets, with user control of thresholding and restriction parameters and visualization options for further refinement. WormSNAP also calculates three types of correlation metrics for 2-channel images, enabling users to select the ideal metric for their dataset. WormSNAP provides robust and accurate fluorescent puncta detection in a variety of conditions, accelerating the image analysis workflow from data acquisition to figure generation.