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Start with a thick brain section that was stained with Golgi-Cox solution to selectively darken neurons and counterstained with cresyl violet to highlight the brain region.
Place them on a slide that has been pretreated with a clearing agent to enhance tissue transparency.
Place the slide on the microscope stage, apply silicone oil, and lower the objective lens until it contacts the oil.
Silicone oil matches the refractive index of the objective lens and slide, enabling detailed imaging.
Focus on the sample, then adjust the camera's exposure and white balance for optimal image quality.
Focus on the top layer to set the upper boundary, then on the bottom layer to set the lower boundary.
Adjust the spacing between images with sufficient overlap to capture details of neuronal projections.
Repeat imaging at different locations to capture areas of interest, then overlay these images to create a three-dimensional representation of the neurons.
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