From sample clearing, to new imaging capabilities, and analysis goals – a multidisciplinary team at the Allen Institute for Neural Dynamics presents the ExA-SPIM pipeline.

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Presentation outline:

1. Introduction | Karel Svoboda, Vice President and Executive Director of the Allen Institute for Neural Dynamics introduces the ExA-SPIM pipeline.
2. Methodology Overview | Adam Glaser, a scientist at the Allen Institute for Neural Dynamics, gives an overview on a new methodology for mapping brain-wide neural circuits.
3. Whole Brain Expansion | Naveen Ouellette, a research associate at the Allen institute for Neural Dynamics describes how to use expansion microscopy techniques to clear and expand whole mouse brain before imaging on the ExA-SPIM.
4. Hardware Introduction | Xiaoyun Jiang, an optical engineer at Allen Institute for Neural Dynamics, describes the hardware involved with ExA-SPIM, provides more details about the system design and show some images taken by the prototype system.
5. SPIM Software Stack | Joshua Vasquez, a systems design engineer at the Allen Institute for Neural Dynamics describes the modular acquisition and production software that runs the ExASPIM microscope and what information is logged.
6. Acquisition UI Overview | Micah Woodard, an optical engineer at the Allen Institute for Neural Dynamics describes the GUI interface to perform imaging acquisition on the ExA-SPIM.
7. Large-scale Data Handling | Cameron Arshadi, a data analyst at the Allen Institute for Neural Dynamics describes measures established to deal with the large datasets produced by ExA-SPIM imaging.
8. Neuron Segmentation | Anna Grim, a scientific data engineer at the Allen Institute for Neural Dynamics describes how Neuron Segmentation can be used to reconstruct individual neurons imaged using the expansion-assisted selective-plane illumination microscopy (ExA-SPIM).