BakingTray
  • BakingTray Documentation
  • Getting Started
    • Hardware requirements
    • Known issues
    • Initial Installation
      • Software installation
      • Setting up ScanImage
    • Hardware setup
      • Motor Setup
        • PI stage setup
        • Calibrating a linear actuator
        • Verifying stage motions
      • Setting up a VT1000 vibratome
      • Setting up the laser
    • Finishing the install
      • Check the noise on your amplifiers
      • Starting BakingTray
      • Settings Files
      • Calibration
        • Basic calibrating procedures
        • Calibrating image size
        • Achieving high stitching accuracy
        • Fine-tuning positioning accuracy
        • Stitching tweak walkthrough
    • Stitching data
  • Users
    • Introduction
    • Sample preparation
    • User Guide
      • Starting BakingTray
      • Step 0: Loading the sample
      • Step 1: Setting imaging parameters
      • Step 2: Preparing the sample
      • Step 3: Selecting the imaging area
      • Step 4: Starting the acquisition
      • Step 5: Concluding the acquisition
      • Setting up checklist
      • Resuming an acquisition
      • Manual ROI acquisitions
    • Excitation choices
    • Choosing imaging settings
    • Troubleshooting
      • Hardware problems
      • Computer problems
      • Cutting problems
      • Imaging problems
    • Data structure
    • autoROI
  • Developers
    • Developers
      • Code overview
      • Developer notes
      • Motion control classes
      • The recipe file
      • Auto-ROI
      • Simulated mode
      • Contributing
    • FAQ
    • Gallery
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  • Seamless 3-D volumes
  • RGB imaging
  • Tracing neurites from single cells
  • Pulvinar neurons projecting to cortical area AL
  1. Developers

Gallery

PreviousFAQ

Last updated 3 years ago

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 .

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.

StitchIt
Pixel size is 2.2 by 2.2 microns and data are a max intensity projection over a small number of planes.
Pixel size along rows is 2.2 microns but along columns is 10 microns. Data are a max intensity projection over a small number of planes.
Pixel size along rows is 10 microns but along columns is 2.2 microns. Data are a max intensity projection over a small number of planes.