Atlas calibration
Use this functionality to calibrate an atlas so that you can match experimental sections with reference sections.Calibration is performed once with one experimental section; it is then applied to the other sections from the same specimen.
Procedure
- Load your image.
- Click Registration>Atlas calibration.
- Select an atlas (we provide Allen atlases by default but you can add your own).
- Define the orientation of your experimental section: Click Change orientation.
- Select the experimental image modality.
For fluorescence:
- Select the channel to be used for registration.
- In the Image adjustment panel (Workspace>Adjustment), select the registration channel to display that channel only in the experimental section.
- Match reference and experimental sections as closely as possible using the Atlas window and the Atlas calibration settings.
- To help with visualizing the two sections, try Show tissue overlay , Use color [...] or adjust transparency with the slider: the closer to Section, the more visible the experimental section; the closer to Atlas, the more transparent the experimental section. In our example, the reference section is a blue overlay and the experimental section is red.
- Navigate in Z to find the closest matching reference section: use the Z slider (drag the slider or scroll the mouse wheel to move along the slider).
- Adjust the scaling (scaling slider) and orientation (shift and rotation sliders) of the reference section so that it matches the experimental section as closely as possible.
- Click automatically refine [...] to finish the calibration.
- To help with visualizing the two sections, try Show tissue overlay , Use color [...] or adjust transparency with the slider: the closer to Section, the more visible the experimental section; the closer to Atlas, the more transparent the experimental section. In our example, the reference section is a blue overlay and the experimental section is red.
- Save your calibration.
Also learn about...
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Copy and paste your atlas files into the ..\ProgramData\MBF Bioscience\Atlases directory.
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Define sectioning plane, sectioning direction, and image orientation.
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By default, the middle reference section is displayed on the left:
- As you move your mouse over different areas of the section, you can see the name of the anatomical structure you're pointing to.
- To zoom in, place the mouse over the section and scroll the mouse wheel.
The reference brain is displayed in 3D on the right; you can rotate it by dragging the mouse.
- The red line indicates the plane location of the reference section shown on the left.
- The yellow sphere indicates the location of the anatomical structure you're pointing to in 2D.