SpyDen: Automating molecular and structural analysis across spines and dendrites

Investigating the molecular composition across neural compartments such as axons, dendrites, or synapses is critical for our understanding of learning and memory. State-of-the-art microscopy techniques can now resolve individual molecules and pinpoint their position with micrometre or even nanometre resolution across tens or hundreds of micrometres, allowing the labelling of multiple structures of interest simultaneously. Algorithmically, tracking individual molecules across hundreds of micrometres and determining whether they are inside any cellular compartment of interest can be challenging. Historically, microscopy images are annotated manually, often using multiple software packages to detect fluorescence puncta (e.g. labelled mRNAs) and then trace and quantify cellular compartments of interest. Advanced ANN-based automated tools, while powerful, are often able to help only with selected parts of the data analysis pipeline, may be optimised for specific spatial resolutions or cell preparations or may not be fully open source and open access to be sufficiently customisable. To address these challenges, we developed SpyDen. SpyDen is a Python package based upon three principles: i) ease of use for multi-task scenarios, ii) open-source accessibility and data export to a common, open data format, iii) the ability to edit any software-generated annotation and generalise across spatial resolutions. Equipped with a graphical user interface and accompanied by video tutorials, SpyDen provides a collection of powerful algorithms that can be used for neurite and synapse detection as well as fluorescent puncta and intensity analysis. We validated SpyDen using expert annotation across numerous use cases to prove a powerful, integrated platform for efficient and reproducible molecular imaging analysis.