> For the complete documentation index, see [llms.txt](https://bakingtray.swcmicroscopy.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://bakingtray.swcmicroscopy.com/general/citing.md). # Citing BakingTray ## How to acknowledge BakingTray and BrainSaw If you have used a BrainSaw rig running BakingTray in your research, you should cite [our methods paper](https://www.biorxiv.org/content/10.64898/2026.09.28.748989v1) and ScanImage. A sentence along the following lines would be a correct acknowledgement: "Samples were imaged using serial two-photon tomography (Tsai et al. 2003; Ragan et al. 2012; Economo et al. 2016) on an open-source (BrainSaw) system running BakingTray (Campbell et al. 2026) and ScanImage (Pologruto et al. 2003; MBF Bioscience)." ## A complete methods description including data pre-processing A more complete methods section should cover the hardware used and how the samples themselves were imaged. The following is a suitable example summary based on the SWC Facility microscopes. It should be adapted to your own hardware. The sample preparation method is generic: you should adapt it to match your actual procedures. Serial two-photon tomography data (Tsai et al. 2003; Ragan et al. 2012; Economo et al. 2016) were obtained on a custom "BrainSaw" ([brainsaw.org](https://brainsaw.org))microscope running BakingTray (Campbell et al. 2026) and ScanImage R2023.1 (Pologruto et al. 2003; MBF Bioscience). Our Facility has three such microscopes; the following is a composite hardware description. A Mai Tai eHP DS laser (Spectra-Physics) was scanned using a 4 kHz or 8 kHz resonant scanner (Cambridge Technology). The beam was focused onto the sample with a Nikon CFI75 LWD 16X W NA 0.8 water immersion objective. Photons were collected using Hamamatsu R10699 multi-alkali PMTs or, in the case of one rig, PDA45 SiPMs from Thorlabs. Data acquisition was controlled by NI DAQ hardware. Up to four detection channels were available, with the following band-pass filters: Far red (BrightLine 676/29), Red (Chroma 605/70m), Green (BrightLine 525/39), Blue (BrightLine basic 460/60). Slicing was performed using a Leica VT1000 section head and tile-scanning was performed with a three-axis stage assembled from PI stages. An Aerotech heavy-duty lift stage pushed the sample up for sectioning. A PI PIFOC allowed for high-speed Z-stacks, and laser power was modulated by a Conoptics Pockels cell. Brains for electrode track tracing were imaged at 4x4x20 microns/voxel (cutting 40 micron sections and imaging two optical planes). Tracks were labelled with DiI, which was excited at 920 nm. We acquired the red channel to visualise the dye and the green channel as a background. We averaged up to two frames and used a laser power of 80 to 120 mW at the sample. Animals were perfused with 4% PFA. Brains were carefully removed from the skull and post-fixed for 24 to 48 hours at 4 °C. Brains were embedded in 5% agarose made up with 50 mM phosphate buffer, which was also used to fill the imaging bath. Slicing was conducted using blades from Campden Instruments (model 752-1-SS), which were changed before each acquisition. Individual tiles were stitched using StitchIt (Campbell et al. 2026; ), which corrected for illumination and generated downsampled stacks to aid analysis. ### Notes * At the SWC, NeuroVision was converted to [Thorlabs PDA45 SiPMs](https://www.thorlabs.com/item/PDA45) in Q2 2026. * All BrainSaw systems with a resonant scanner use one from Cambridge Technology. * Some BrainSaws use a vDAQ data acquisition system (it has a black breakout box). * You can add the BakingTray version number by referencing the commit cited in one of your recipe files. * The MATLAB version is also recorded in the recipe files, should you want to add those. ## References * Campbell et al. 2026, [bioRxiv](https://www.biorxiv.org/content/10.64898/2026.09.28.748989v1) * Economo et al. 2016, eLife, * Pologruto et al. 2003, Biomed Eng Online, * Ragan et al. 2012, Nature Methods, * Tsai et al. 2003, Neuron,