Hardware requirements

This page describes the hardware you ought to have to run BakingTray using ScanImage.

Acquisition PC

If you're building from scratch, buy the fastest Intel-based computer you can. Prioritise CPU speed over number of cores, since ScanImage runs single threaded. Otherwise, any moderately fast PC should work.
We acquire images to a local RAID array: four platter drives in RAID 1+0. The striping is necessary when using a resonant scanner. Unless you anticipate very large datasets, 4 TB drives should be sufficient.
Hardware of course goes out of date quickly, but the following is an example of a successful configuration for resonant scanning.
  • i7-6700K @ 4 GHz, 16 GB DDR4-2133 MHz RAM, H170-Pro motherboard
  • Adaptec RAID 6405E, 4x WD Black RAID 1+0.
  • NVIDIA GeForce GT 730 to drive a pair of DELL U2715H monitors. Otherwise the on-board graphics are fine.
  • Oxford Semiconductor 4 port PCIe serial adaptor for PIFOC and motion control hardware (laser comms via motherboard serial port).
A PCIe serial adapter card will have a lower latency than USB-serial and so is preferable. Install the card in the lowest bus number possible on your motherboard. If you do not do this, Windows will re-assign COM port numbers when you change other hardware (e.g. swap out or move an NI card in the chassis).
The hardware RAID above is necessary as a single platter drive won't provide enough bandwidth for resonant scanning. You don't need RAID for galvo scanning. You can substitute a single SSD for resonant scanning. Samsung currently make 8 TB SSDs with a warranted life of 3 years or 2,880 TB.

Data acquisition devices

BakingTray works with any scanning hardware and acquisition cards supported by ScanImage. For resonant scanning with four channels we use:
  • Chassis: NI PXIe-1073
  • Image acquisition: NI PXIe-7961R FPGA and NI-5734 digitizer
  • PIFOC, Pockels, and scan control: 3x PXIe-6341
  • PMT control: NI USB-6343 (overkill, but it was the easiest option)

Galvo scanning DAQs

We have run galvo/galvo using both NI PCI-6110 and NI PCI-6115 acquisition cards. However, PXIe devices are recommended as they're easier to manage in a chassis. The PXIe-6124 has also been tested but higher sample speeds don't work on all motherboards.

Scanning Hardware

  • We recommend resonant scanning as it is much faster for high resolution images even though there is an increase in shot noise due to the shorter dwell time. You can compensate for the shorter dwell time by increasing laser power and using moderate PMT gains. Averaging frames is also possible. Unlike linear scanning at short line periods, the bidirectional "comb" artifact is virtually gone with resonant scanning. Both 12 kHz and 8 kHz resonant scanners will work. 8 kHz are recommended because of the larger field of view. The larger FOV means fewer stage motions and so imaging times do not increase compared with the 12 kHz, despite the increase in dwell time.
  • A 400 micron travel range PIFOC (we use a P-725.4CDA) is recommended for optical sectioning. Shorter travel ranges would also be acceptable if you don't plan on imaging cleared tissue.
  • You will need a Pockels cells to ramp laser power with depth. Choose one with a low dispersion crystal.

The microscope

You ideally want a microscope capable of imaging a large FOV (>1 mm) that is flat and undistorted. The FOV affects scanning speed: if you have a smaall FOV the tile scanning becomes slow. For our purposes a flat field would be one with less than 10 microns of sag in focal plane. If you lack this, everything will still work but it can be trickier to get good overlap of features at tile edges. "Distortion" refers to pincushion and barrel distortion: the less of this the better. Again, you can work with a microscope that exhibits it. We care about distortion because it affects tile overlap areas when stitching images (although some degree of correction is possible).
You can image an EM grid such as the 2145C from 2spi to assess FOV and distortion. For field flatness tou can take a z-stack through one of these slides, or make your own by cover-slipping a small drop of fluorescein solution.
You will want at least a manual coarse focus stage with 20 mm of travel for the objective. Ideally a motorized coarse z stage: this is easier to use.
For objectives: a Nikon 16x NA 0.8 objective works well and you don't need to spend more to get good results unless you are planning on routinely imaging fine structures (under about one micron).


BakingTray interacts with the laser to turn it off at the end of acquisition and stop acquisition if the laser fails to modelock. The system has been well tested with MaiTai and Chameleon lasers. We've run these rigs with both Spectraphysics and Coherent lasers and don't have a strong preference. If you don't have a relay between the scanners and your Pockels cell doesn't introduce too much GDD (they vary by crystal composition) then a pulse compressor isn't critical.
The system can run with multiple lasers simultaneously, since this is supported by ScanImage. However, BakingTray currently only monitors the modelock state of one laser. There is no facility currently for re-imaging sections at a different wavelength or with a different laser.

Motion Hardware

The sample sits in a water bath atop an X/Y/Z stage.
PI stages are recommended and likely any stages from PI will be supported out of the box. BakingTray is modular, so it's easy to add classes to support stages from other manufacturers.

The stage

You will need a functioning and heavy-duty 3-axis stage. This stage will translate the sample in X/Y for tile scanning and also raise it in Z and move in X for slicing. The sample stage will be controlled by BakingTray, not ScanImage. Motions in the X/Y plane need to be as fast and accurate as possible, since the microscope spends much of its time just moving the sample.
Known to work well are the PI V-551 direct-drive stage and C-891 controllers. We use 130 mm of travel for X and 60 mm of travel for Y.
Also known to work are PI V-508, PI M-531.DD, and PI M-605.2DD.
The vertical stage (Z-jack) is a little more tricky. A DRV014 from ThorLabs will work as a Z-jack with the BSC201 controller, but this is hard to mount and the API for the BSC201 is pretty annoying to work with. A better option is likely to buy a lift stage from Aerotech. An AVS-100 with 25 mm of travel will work. Better yet, a PRO190SV-035 or PRO190SV-050.
BakingTray is highly modular, and it's fairly easy to modify the software to use stages from other vendors will require a little coding to set them up.

Constructing the XYZ stage

The X/Y stages can be mounted directly on top of an AeroTech lift stage (you will need to machine a coupler). The AeroTech stage can in turn be mounted on a breadboard with three ThorLabs BLP01 adjustable height legs for tilt correction.


You can use any vibratome. The vibratome can be gated either via TTL or with a FaulhaberMCDC serial-based DC motor controller. A nice option is a Leica VT-1000 vibratome head and blade, which can be purchased as spare parts from the manufacturer. The vibratome does not need a linear motor: it will not translate, the slicing is all done by the XYZ stage. You should mount the vibratome in a way that allows you to control the roll axis of the blade.