Testing the Prime95B – a back-illuminated sCMOS camera with 95% QE

A few weeks ago I mentioned that Photometrics had released a new camera, the Prime95B, featuring a back-illuminated sCMOS sensor with 95% peak QE. I got a chance to play with it last week, and I’m pleased to say that it performs as well as you would expect. We compared it to an iXon 888 EMCCD mounted on our CSU-W1 spinning disk confocal. We had purchased this EMCCD for imaging those samples that were too dim to get good images with the Zyla 4.2 sCMOS camera we also have mounted on the confocal. (You can see a sketch of how everything is configured in this previous post). For testing the Prime95B, we replaced the Zyla 4.2 with the Prime95B, allowing us to directly compare the Prime95B and the iXon 888.

Before I get to the data, however, what performance do we expect? To get a sense of what to expect I wrote a Matlab script that calculates the theoretical performance for a number of different cameras, using their quantum efficiency, read noise, and excess noise factor (for EMCCDs). You can get the script here.   You can read more about how to calculate the signal-to-nosie ratio for a camera in this Hamamatsu white paper. Here, I’m ignoring the different pixel sizes of the various cameras by assuming that they all receive the same photon flux per pixel, as if the magnification had been adjusted to produce the same effective pixel size at the sample.

Theoretical performance of different cameras.

Theoretical performance of different cameras. Ideal is a theoretical ideal camera with QE=1 and no read noise. EMCCD assumes a high EM gain, ~200x; 82% QE sCMOS is a Flash4.0v2 or Zyla 4.2 Plus; 72% QE sCMOS is a Flash 4.0 or Zyla 4.2; ICX285 is a Coolsnap HQ2 or similar interline CCD camera.

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USB3 Flash drives for high speed data transfer

In the past few years, we’ve switched the NIC almost exclusively to sCMOS cameras. We still have a few EMCCDs, but we have no interline CCDs in the NIC anymore. This change has greatly increased data acquisition rates – we’ve gone from 1.4 megapixel images to 4+ megapixel images. It’s now very common for someone to sit down at a microscope for a few hours and end up with 20 GB of data, and time lapse experiments often produce 1 TB.

This increase in the amount of data has made data transfer a bottleneck. USB2.0 flash drives, in our experience, top out around 20-30 MB/sec transfer rates. At that speed, a 20 GB data set takes 10-15 minutes to transfer. To reduce this time, we’ve begun to upgrade all of our PCs to add USB3 ports. We’ve been using Startech cards and have had good luck with them. With a good USB3 thumb drive – we use a SanDisk Extreme for testing – we can get transfer speeds of ~180 MB/sec, a 6-8x improvement in speed. In the process of doing this I’ve learned a few useful things. First, USB2 cables do not support USB3 transfer speeds – you need to have a USB3 cable. Second, not all USB3 hubs are equal – we have one that doesn’t manage USB3 transfer speeds. We’ve had good luck with this Anker USB3 hub. Finally, some devices (in particular the Nikon Ti) do not like to run over USB3 ports, so you still need some USB2.0 ports for controlling hardware.

We also have a network server for data transfer, but with gigabit ethernet, it maxes out at about 100 MB/sec transfer speeds, so the USB3 drives end up being somewhat faster. We’re hoping that the USB drives will be reliable enough to allow direct acquisition of data to them (rather than saving to the local hard drive and then copying), although we haven’t tried that yet. We have had problems with transfer glitches causing experiments to be interrupted when we save over the network or to USB2.0 drives, so we don’t recommend that.

There is now a USB3.1 Gen 2 specification that promises a 2x speed improvement over USB3.0, but very few drives support it, so we haven’t started looking at that.