A deep learning algorithm for 3D cell detection in whole mouse brain image datasets
Fig 1
Simplified schematic diagram of the serial two-photon microscope and data acquisition process.
A: The tissue is excited using a femtosecond Ti-sapphire laser (emission wavelength = 800 nm). For data collection, 50 μm of tissue (at approximately 40 μm to 90 μm below the tissue surface) is imaged in ten, 5 μm thick planes. An in-built microtome then physically removes a 50 μm thick section from the optical face. This process is repeated to generate a complete 3D dataset of the specimen. B: For signal collection, the emitted lightpath is split into two channels whereby the primary channel detects the fluorescence signal of interest from labelled cells (e.g. mCherry at 610 nm) and the second channel (e.g. at 450 nm) detects the tissue autofluorescence signal that reveals gross anatomical structure.