> 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/getting-started/build_overview.md).

# Build overview

Planning your BrainSaw build

This is a high-level overview of the steps required to assemble a BakingTray-based STPT system. Other pages on the site provide more detail. There is no complete end-to-end set of build instructions, but groups have successfully used what is on here to autonomously build a BrainSaw.

## Step 1: Decide on your build path

If you have good general tech skills and enjoy building stuff, you can probably build a BrainSaw STPT system. There are several paths to assembling a system, and there is likely one to fit your skill-set.

1. Modify an existing two-photon microscope
2. Upgrade a [legacy TissueCyte 1000](/getting-started/tissuecyte_upgrade.md) system from TissueVision
3. Buy a suitable new two-photon microscope from a trusted vendor and add serial section capability to that
4. DIY the entire build yourself from scratch

The SWC AMF can provide advice and potentially even hands-on assistance for your build. Contact [Rob Campbell at the SWC AMF](https://swcmicroscopy.com/people/) to register your interest.

## Step 2: Gather the parts

The components can be collated and tested in parallel.

* Put in place a suitable acquisition PC with ScanImage.
* Put in place the two-photon microscope, ensuring space for the stages and slicing hardware.
* [Quantify microscope performance](https://pmc.ncbi.nlm.nih.gov/articles/PMC7618499/), measuring FoV, field homogeneity, PSF, laser power, etc. See also [MPQC](https://github.com/SWC-Advanced-Microscopy/multiphoton-qc).
* [Assemble the vibratome](https://github.com/SWC-Advanced-Microscopy/Brainsaw_CAD/tree/main/CAD/Vibratome) and associated hardware. Test these.
* Assemble the X/Y/Z stage and test.
* Make the [water bath](https://github.com/SWC-Advanced-Microscopy/Brainsaw_CAD/tree/main/CAD/Water_Bath).
* Set up an [analysis PC for stitching](/getting-started/stitching.md) with StitchIt.

For further information on parts see [hardware requirements](/getting-started/hardware_requirements.md).

## Step 3: Assemble

* [Install the software](/getting-started/initial-installation/installing_software.md) and [set up ScanImage](/getting-started/initial-installation/setting-up-scanimage.md).
* Get BakingTray communicating with the [stages](/getting-started/hardware-setup/motor-setup/verifying_stage_operation.md), [laser](/getting-started/hardware-setup/laser_setup.md), and [vibratome](/getting-started/hardware-setup/setting_up_vt1000.md), then [fill in the settings files](/getting-started/finishing-the-install/starting-bakingtray-for-the-first-time.md).
* Use MPQC and BakingTray to [calibrate laser power](/getting-started/initial-installation/setting-up-scanimage.md#displaying-power-in-mw-in-scanimage) in ScanImage at the wavelengths you plan to use often. We normally calibrate at 770, 800, 920, 950, and 1040 nm.
* Clamp the water bath into the X/Y/Z stage. Set the X/Y stages to their mid-points (0 mm) and centre the frosted part of a slide under the objective.
* Set the X, Y, Z limits of the stages in BakingTray so the objective can not hit any part of the bath.
* [Level the stage platform](/getting-started/finishing-the-install/calibration/basic-calibrating-procedures.md) using a thin fluorescent slide.
* Ensure the X and Y stage axes move the sample along the scan axes.
* [Calibrate the number of microns per pixel](/getting-started/finishing-the-install/calibration/calibrating-the-number-of-microns-per-pixel-with-scanimage.md) and set up the image sizes in `frameSizes.yml`.
* [Position the vibratome](/getting-started/hardware-setup/positioning_the_vibratome.md), add the blade holder, and update the stage limits.
* Use fluorescent agarose to adjust blade angle. This is also a chance to test slicing.
* Enter the [blade and slide positions](/getting-started/finishing-the-install/the-settings-files.md#how-to-set-the-blade-and-stage-position-values) into the system settings file.
* Run test samples and [fine-tune stitching accuracy](/getting-started/finishing-the-install/calibration/achieving-high-stitching-accuracy.md).