
Scientific Overview | ExA-SPIM
A high-level explanation of the protocols necessary to implement the Expansion Selective Plane Illumination Microscopy (ExA–SPIM) pipeline
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.
Presentation outline:
- Introduction | Karel Svoboda, Vice President and Executive Director of the Allen Institute for Neural Dynamics introduces the ExA-SPIM pipeline.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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).