High-throughput serial two-photon tomography with BakingTray and BrainSaw
Abstract
Volumetric imaging is increasingly important in fields such as neuroscience, where quantifying structure and mapping features are inherently three-dimensional problems. Block-face serial two-photon tomography (STPT) has emerged as a powerful approach for high-resolution, whole-organ volumetric imaging. STPT avoids complex sample preparation and balances image quality, speed, and scalability. However, STPT remains niche, in part because of the absence of flexible, general-purpose control software. Here we present
BakingTray, an open-source software platform for STPT that extends ScanImage. BakingTray's modular framework accommodates diverse hardware configurations and allows users to build systems customised to their needs. Twelve such systems, which we call 'BrainSaws', have been constructed worldwide since 2016, with more under construction, and have so far contributed to 35 research papers. The three systems at the Sainsbury Wellcome Centre alone have acquired over 7,000 samples in a busy multi-user facility. We demonstrate the platform across its core neuroscience applications: electrode track localisation, brain-wide cell counting, and bulk projection mapping. Beyond these, we map the cell-type-specific synaptic output of inhibitory neurons in the ventral lateral geniculate nucleus and, with whole-mount staining, amyloid plaques brain-wide in a mouse model of Alzheimer's disease. BakingTray is a mature platform for groups or facilities needing a customised volumetric imaging solution, whether built new or converted cheaply from an existing two-photon microscope.
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BibTeX
@misc{campbell2026highthroughput,
title = {{High-throughput serial two-photon tomography with BakingTray and BrainSaw}},
author = {Robert Aa Campbell and Kurt I Anderson and Asli Ayaz and Emmanuel Beaurepaire and Hugo Blanc and Antonin Blot and Juan Carlos Boffi and Vincent Bonin and Howard Hw Chan and Beverley Clark and Georgios Foustoukos and Peter Gordon and Del Halpin and Yunyun Han and Michael Hausser and Sonja B Hofer and Friedrich W Johenning and Stephan Junek and Loukia Katsouri and Michael Krumin and Pierre Mahou and Troy W Margrie and Adrien Philippon and Viktor M Plattner and Claudio Polisseni and Solene Prudhomme and Rajeev Rajendran and Simon Townsend and Nicole Vissers and Florian Vollrath and Simon Weiler},
howpublished = {HAL},
year = {2026},
month = sep,
doi = {10.64898/2026.09.28.748989},
url = {https://hal.science/hal-05776623v1},
note = {CC BY 4.0},
}
RIS
TY - UNPB
TI - High-throughput serial two-photon tomography with BakingTray and BrainSaw
AU - Robert Aa Campbell
AU - Kurt I Anderson
AU - Asli Ayaz
AU - Emmanuel Beaurepaire
AU - Hugo Blanc
AU - Antonin Blot
AU - Juan Carlos Boffi
AU - Vincent Bonin
AU - Howard Hw Chan
AU - Beverley Clark
AU - Georgios Foustoukos
AU - Peter Gordon
AU - Del Halpin
AU - Yunyun Han
AU - Michael Hausser
AU - Sonja B Hofer
AU - Friedrich W Johenning
AU - Stephan Junek
AU - Loukia Katsouri
AU - Michael Krumin
AU - Pierre Mahou
AU - Troy W Margrie
AU - Adrien Philippon
AU - Viktor M Plattner
AU - Claudio Polisseni
AU - Solene Prudhomme
AU - Rajeev Rajendran
AU - Simon Townsend
AU - Nicole Vissers
AU - Florian Vollrath
AU - Simon Weiler
PY - 2026
DA - 2026/09/28
PB - HAL
DO - 10.64898/2026.09.28.748989
UR - https://hal.science/hal-05776623v1
AB - Volumetric imaging is increasingly important in fields such as neuroscience, where quantifying structure and mapping features are inherently three-dimensional problems. Block-face serial two-photon tomography (STPT) has emerged as a powerful approach for high-resolution, whole-organ volumetric imaging. STPT avoids complex sample preparation and balances image quality, speed, and scalability. However, STPT remains niche, in part because of the absence of flexible, general-purpose control software. Here we present BakingTray, an open-source software platform for STPT that extends ScanImage. BakingTray's modular framework accommodates diverse hardware configurations and allows users to build systems customised to their needs. Twelve such systems, which we call 'BrainSaws', have been constructed worldwide since 2016, with more under construction, and have so far contributed to 35 research papers. The three systems at the Sainsbury Wellcome Centre alone have acquired over 7,000 samples in a busy multi-user facility. We demonstrate the platform across its core neuroscience applications: electrode track localisation, brain-wide cell counting, and bulk projection mapping. Beyond these, we map the cell-type-specific synaptic output of inhibitory neurons in the ventral lateral geniculate nucleus and, with whole-mount staining, amyloid plaques brain-wide in a mouse model of Alzheimer's disease. BakingTray is a mature platform for groups or facilities needing a customised volumetric imaging solution, whether built new or converted cheaply from an existing two-photon microscope.
ER -