Comprehensive software suite for functional analysis and synaptic input mapping of dendritic spines imaged in vivo.

Significance: Advances in genetically encoded sensors and two-photon imaging have unlocked functional imaging at the level of single dendritic spines. Synaptic activity can be measured in real time in awake animals. However, tools are needed to facilitate the analysis of the large datasets acquired by the approach. Commonly available software suites for imaging calcium transients in cell bodies are ill-suited for spine imaging as dendritic spines have structural characteristics distinct from those of the cell bodies. We present an automated tuning analysis tool (AUTOTUNE), which provides analysis routines specifically developed for the extraction and analysis of signals from subcellular compartments, including dendritic subregions and spines. Aim: Although the acquisition of in vivo functional synaptic imaging data is increasingly accessible, a hurdle remains in the computation-heavy analyses of the acquired data. The aim of this study is to overcome this barrier by offering a comprehensive software suite with a user-friendly interface for easy access to nonprogrammers. Approach: We demonstrate the utility and effectiveness of our software with demo analyses of dendritic imaging data acquired from layer 2/3 pyramidal neurons in mouse V1 in vivo. A user manual and demo datasets are also provided. Results: AUTOTUNE provides a robust workflow for analyzing functional imaging data from neuronal dendrites. Features include source image registration, segmentation of regions-of-interest and detection of structural turnover, fluorescence transient extraction and smoothing, subtraction of signals from putative backpropagating action potentials, and stimulus and behavioral parameter response tuning analyses. Conclusions: AUTOTUNE is open-source and extendable for diverse functional synaptic imaging experiments. The ease of functional characterization of dendritic spine activity provided by our software can accelerate new functional studies that complement decades of morphological studies of dendrites, and further expand our understanding of neural circuits in health and in disease.

The Cousa objective: a long-working distance air objective for multiphoton imaging in vivo.

Multiphoton microscopy can resolve fluorescent structures and dynamics deep in scattering tissue and has transformed neural imaging, but applying this technique in vivo can be limited by the mechanical and optical constraints of conventional objectives. Short working distance objectives can collide with compact surgical windows or other instrumentation and preclude imaging. Here we present an ultra-long working distance (20 mm) air objective called the Cousa objective. It is optimized for performance across multiphoton imaging wavelengths, offers a more than 4 mm2 field of view with submicrometer lateral resolution and is compatible with commonly used multiphoton imaging systems. A novel mechanical design, wider than typical microscope objectives, enabled this combination of specifications. We share the full optical prescription, and report performance including in vivo two-photon and three-photon imaging in an array of species and preparations, including nonhuman primates. The Cousa objective can enable a range of experiments in neuroscience and beyond.