Tested Hardware

Example hardware specs

We are using the following hardware in our Windows 7 acquisition machine to acquire images with resonant scanning:

• i7-6700K @ 4 GHz, 16 GB DDR4-2133 MHz RAM, H170-Pro motherboard
• Data acquired to: Adaptec RAID 6405E, 4x WD Black RAID 1+0 (Windows software RAID using the motherboard should also work and may be preferable).
• Image acquisition, Pockels control, PIFOC control: NI PXIe-1073, PXIe-6124 with NI 5734, 3x PXIe-6341
• PMT control: NI USB-6343 (overkill, but it was the easiest option)
• 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).

Scanning hardware

All scanning hardware supported by ScanImage should work. Additionally, we can confirm that the system has been tested with the following:

• Galvo/galvo mode has been tested extensively using 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.
• Resonant scanning is known to work with an NI PXIe-7961R and both the 2-channel NI 5732 and the 4-channel NI 5734 digitizers.
• Both 12 kHz and 8 kHz resonant scanners will work. 8 kHz are recommended because of the larger field of view and slightly better image quality. The larger FOV means fewer stage motions and so imaging times do not increase compared with the 12 kHz.
• Of course PIFOCs (we use a P-725.4CDA) and Pockels cells both work.
• We use an NI USB-6343 to control the PMT gains. This works but we see the following bug: there is a rare chance that, when BakingTray is open, switching off the PMTs causes MATLAB to crash. We work around this by disabling PMT auto-on and having BakingTray issue the PMT off command at the conclusion of acquisition. We experience no problems or acquisition failures when working like this.

Lasers

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.

Motion control hardware

• X/Y stage control tested with PI V-551 (C-891 controller), PI V-508 (C-891 controller), the Newport EPS300 controller has been tested but the code has not been maintained since about 2016.
• Z stage control tested with ThorLabs DRV014 actuators (BSC201 controller), which works reliably with some minor hiccups sometimes occurring when connecting to the controller. However, in general ThorLabs motion controllers are not recommended as the Kinesis interface does not work in MATLAB (even though it's advertised as doing so), leaving only the APT interface which is buggy and annoying. Also tested and working is the PI L-310.20SD driven by a C-663 controller. Note the load restriction on the L-310. With minimal addition work BakingTray will be able to control the beefy vertical stages from Aerotech. An AVS-100 with 25 mm of travel will work. Better yet, a PRO190SV-035 or PRO190SV-050. The Aerotech stages are probably the best option at present.

Vibratome

Any vibrotome that can be activated using a TTL pulse will work. Control of the DC motor driving the vibrotome on the TissueCyte has been tested briefly but we prefer the Leica VT1000.