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. 2023 Jun 29;21(6):e3002158. doi: 10.1371/journal.pbio.3002158

Fig 16. The Nissl and backlit registration pipeline.

Fig 16

(a) For every 10th STPT tissue section, we take an additional backlit and a Nissl image with a second microscope. (b) Each time a section is moved or stained, it undergoes physical deformations. We established a robust image registration pipeline that reliably aligns the Backlit/Nissl images with the STPT images in a fully automated manner. (c) An example of a backlit image section before and after alignment. (d) After mapping the Nissl/Backlit images of our entire population to the STPT reference template, we computed population averages. STPT, serial two-photon tomography.