Hardware

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

Computer

Buy the fastest Intel-based computer you can. Prioritise CPU speed over number of cores, since ScanImage runs single threaded.

We acquire images to a local RAID array: four platter drives in RAID 1+0. Unless you anticipate very large datasets, 2 TB or 4 TB drives should be sufficient. This should ideally be set up using the built-in motherboard RAID, to keep the slots free. Consult your motherboard manual and set the on-board SATA ports to RAID mode if necessary before installing Windows. Windows is stupid and fails to boot if you switch to RAID mode afterwards. In the event that you do need to switch SATA mode and Windows complains (it will likely BSOD) then you can try the following

Just boot it into safe mode and it should automatically install the RAID drivers. After booting into safe mode once it should then be able to boot normally. If this fails, check whether the RAID drivers are installed (look on motherboard manufacturer' website and download the drivers) then try again.
http://www.askvg.com/how-to-change-sata-hard-disk-mode-from-ide-to-ahci-raid-in-bios-after-installing-windows

Data acquisition devices

See the ScanImage docs to figure out what data acquisition devices you need.

Scanning Hardware

BakingTray works with any scanning hardware and acquisition cards supported by ScanImage and has been tested with both linear and resonant scanning. 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 decreasing PMT gain. Averaging frames is also possible. Unlike linear scanning at fast line periods, the bidirectional "comb" artifact is virtually gone with resonant scanning. In addition, we find ScanImage interacts better with BakingTray when running in resonant mode. An 8 kHz scanner is recommended. You ideally want a microscope with large FOV (>1 mm) that is flat and undistorted. However, the exact specs will depend on what you are trying to image.

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

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 3-axis stage. For the X/Y plane, a V-508 or V-551 stages from PI are strongly recommended. The larger, more heavy-duty, V-551 stages are better. Other PI stages with suitable travel range will also work. Stages by other vendors will require a little coding to set them up. You want the stages to be fast because the system spends a lot of time moving. 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.

Vibratome

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.

Fast Z focusing

You will likely want to image multiple optical planes for each physical section. To do this you will want a PIFOC or some other way of rapidly moving the focal plane. Whatever you choose, it must be controllable with an analog input. You will need an NI 6321 or 6341 to control the fast Z device with ScanImage.

Modulating laser power

If you wish to modulate laser power with depth or blank the beam turn-arounds you will need a suitably fast modulator. A Conoptics Pockels cell is suitable. The device must be controllable via an analog input. ThorLab's LCVR controllers are not suitable. If you want to use an LCVR you will need to build your own amplifier. You will need an additional NI 6321 or 6341 to control the beam intensity.