The following is an example image obtained with the software. The image is obtained using tile-scanning with a 12 kHz resonant scanner. Tile illumination artifacts have been removed during image assembly by StitchIt.

Seamless 3-D volumes

BakingTray can produce seamless 3-D volumes. This is a movie of a mouse brain which was injected with a GFP viral tracer. The the grey shows background fluorescence.

RGB imaging

The following movie was obtained using tdTomato, GGP, and BFP. Sample imaged at 790 nm using a 2-photon laser. Sections taken every 25 microns. Artifacts arise from the very thin sections that sometimes float between the sample and the objective.

Tracing neurites from single cells

Moving showing single cortical neurons expressing GFP after plasmid electroporation.

Pulvinar neurons projecting to cortical area AL

These maximum intensity projections come from data generated by Ioana Gasler. They are RetroAAV cre in AL and flex mCherry in the pulvinar. Data were acquired at 2.2 x 2.2 x 10 µm. Images are max intensity projections of the full volume along different axes, with a bit of Gaussian blur for smoothing (sigma = 1 µm). The volume shown is roughly 4.7 x 3.6 x 6.0 mm (ML x DV x AP). Note that despite the relatively large step size (10 µm) between optical planes, it is easy to follow the single axons.

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