Category: Photometrics

  • 95% QE SCMOS vs. EMCCD

    In 2011, I reviewed the Andor Neo, one of the first scmos cameras commercially available. I ended my report with this statement,

    “…there is much life left in the good old frame transfer sensor…until someone cooks up a back thinned scmos…”

    Recently, back thinned scmos camera have come to market, and Kurt Thorne at the UCSF NIC has an excellent report on Photometrics’ new Prime 95B camera. While there may be specific areas of research that can benefit from a BT EMCCD, it looks like the days of EMCCD are at an end for most of us. I guess the question now is, what comes next?

    -Austin

     

     

  • How to use external triggers on scientific and industrial cameras

    Controlling a camera from an external trigger can be very useful. External triggering provides greater timing accuracy, direct control over exposure duration, and remote operation from TTL devices. This is a prime reason I made the Triggerscope controller, so I though it would be useful to explain how this works and what you can do with it.

    What is “triggering”?

    Most cameras built for scientific imaging or life science have a high density connector located on the back. 90% of the time, this is only used by savvy customers, or OEM integrators (companies buying a camera to place inside a machine for resale). The connector on the back of the camera will typically include 2 basic functions: Inputs (connections which send signals into the camera) and outputs (signals which activate when the camera is in a process or cycle).

    Why use Triggering on a camera? Doesn’t the software control image capture?

    Of course, software can tell a camera to snap an image. But when will that image be captured? Software needs to do more than say “snap” when you capture an image. Behind the scenes, a LOT of stuff happens!

    • the top level controls you see are converted into camera-specific commands via the camera “device driver” in your software.
    • The camera commands are fed into a control card or USB port and up to the camera.
    • The camera accepts the commands, which activate sets of tables in the camera firmware, to set up a sequence of turning on and off clocks and transistors at very high speed, all depending on your binning, ROI, etc.
    • The camera performs the above operations, and sends back an image.

    What is quickly apparent is how much has to happen to get an image. In addition, the camera firmware will process some instruction sets faster than others! So some exposures might come back 200ms from issuing the “snap” button, while others will return in 130ms, 30ms, who knows!

    So when precise timing is desired, and you really want that camera to fire at a specified time, triggering may be used. In this configuration, all software comms with the camera are pre-compiled, everything’s done. All of the steps above are performed, but the last step, the “camera performs operations above” sits….and waits…for the trigger line to run from 0 Volts to 5 Volts. As soon as that happens, an image is captured.  For single frames, this is somewhat useful, but for sequences, this is great. We can capture images at some interval with 100% confidence timing is accurate.

    Example

    Let’s look at a typical camera, and pull the information we need from the user manual, in order to better understand triggered control. For this post, I’ll use the Photometrics CoolSNAP MYO camera, and as Photometrics makes it easy to read up on the user manual for their products, you can find the user manual here.  Page 21 of the PDF describes the various operating modes for the trigger input. Note, the PDF also gives us information on EACH PIN used in conjunction with input and output signaling. There’s more than one!

    Screen Shot 2016-01-15 at 2.33.15 PM

    Note, PM also provides short descriptions for each pin:

    Screen Shot 2016-01-15 at 2.33.29 PM

    So – now we know which pins communicate which functions from the camera head connector – to connect to any of these, we’d simply connect a ground wire, and a positive pin wire to our chosen camera pin (for our needs, say Pin 1 – Trigger In)

    Now – the most pertinent for us is the trigger in line, which runs in a few modes.  Let’s review each, and why we might use them:

    Trigger-First (sometimes called other things like “Fire”)

    In this mode, the camera is set to snap some # of images (let’s say 10), but waits for a trigger input. Once that input goes high, the camera snaps 10 images as quickly as possible.

    Strobe

    In this mode, the camera is again configured for some # of images, but every image waits for a trigger.

    Bulb

    In this mode, the exposure time for each image is controlled by the input trigger. Again, multiple images are assumed (although Image qty of 1 is acceptable), and each frame waits for a trigger input pulse.

    These three modes constitute the majority of uses for a typical triggered input line.

    So, what does “receive a trigger” actually mean? Good question!

    Triggering = TTL Control

    Cameras, like almost all computer systems, are made to interact with external systems. One of the oldest, and most common methods, is referred to as “transistor transistor logic” or TTL. This boils down to the concept that if we specify an electrical voltage value of X as “off” and Y as “ON” then we can remotely flip a switch.

    Many imaging devices use this communication method. A simple uniblitz shutter for example, can accept USB/serial data to open and close the shutter, but using TTL is faster and simpler. (just one thing to do, send 5Volts or 0Volts.) Below is an oscilloscope capture of such a signal. The vertical scale = Voltage level, and the horizontal scale from left to right = time elapsed. My annotations are in red. Note the yellow line, which indicates the signal.

    ttl_example

    Example Signal

    Let’s say we have a device, for now, it’ll be the triggerscope 2, which is connected to the “TRIGGER” line of our camera. We want to signal the camera to capture immediately after we turn on an LED. In this case, we might use the triggerscope line 1 for the LED on and off, and line 2 for the camera signal.

    In our software, we’d specify the camera exposure time, binning, and other usual parameters. In our controller, we’d set the output to high when we wanted to capture our image. Let’s use an example of 1 image:.

    Tell the camera to acquire using software (nothing should happen yet!)

    -Camera waits for a trigger signal

    Tell our triggerscope to send a TTL high

    -Camera captures an image.

    Tell our triggerscope to send a TTL low

    (nothing changes)

    The above sequence can be used for a series of images. In that case, the acquisition would be configured for some # of frames (say 10), and the camera would capture 1 frame each time the signal swung from low to high.

    To tie everything together, I’ve recorded  quick video explaining this on the scope. Check it out!

    [youtube width=”600″ height=”365″ video_id=”4KNe5GxpuOo”]

    So – now you know how cameras can be controlled via TTL – if anyone has questions please comment below, so I can address them. Thanks!

    -Austin

     

     

     

  • WHY YOU SHOULD ATTEND THE UCSF/QB3 Microscopy Course

    Over the course of my career, I’ve flown across the US to attend a variety of imaging related instructional courses, all on the eastern seaboard. We are all familiar with the Woods Hole courses, the AQLM course, and so forth. What has boggled my mind is that here I am in the SF Bay area, surrounded by arguably the most densely populated and diverse centers of biological science innovation on earth, and there’s no major course?

    I started pestering the owners of Technical Instruments about this one night, and they admitted the same question had long been on their minds. A few months later, we asked the NIC team at UCSF about it, and found to our surprise that they were already cooking something up. We offered to help as needed, and have been doing what we can to help support the course ever since.

    So, UCSF/QB3 has just published their official webpage for the inaugural Microscopy and Imaging Course for 2012. (They let me design the website, I hope you like it!)

    If you are a regular reader of my blog, I’ll assume you’re involved enough in imaging that you would stand to gain much from attending the course. This won’t be a “sit in classes all day” kind of deal. The course has been designed around a kinesthetic approach, with lectures taking roughly 50% of the time, and the other 50% being hands-on bench work.

    If you live far away, or are having a rough funding year, please apply for a stipend for either the course tuition and/or travel. One of the initial course goals is to host the most geographically and vocationally diverse student group possible. So if you are thinking, “my work doesn’t fit the norm for the life science community” or “I’m not from one of the major research centers”, then you should apply!

    I’ll be attending to support the course along with most of our outside team from TI. I hope to see you there!

    -Austin

  • How to Align a Dualview 2

    Walking through the alignment procedure of the DV 2, narrated by Jeff Harris from Photometrics . Great video and great explanation Jeff! For those of you who have a DualView, I’m certain this video will come in handy.

    httpv://www.youtube.com/watch?v=WJC5_DdaH80

     

  • Acquisition crashes, and power settings in Win7

    Windows 7 has a new power management interface, and the design of modern motherboards, along with win7 Automatic Power Management (APM), can cause some insidious device-based software crashes if power options aren’t set correctly. Here’s how to make sure your system is running in the best mode.

    • Open the Windows Control panel
    • Search for and open “Power Options”

    • You’ll see a “power plan” like the one below. Click the “Show Additional Plans” button, and check the radio button for the “High Performance” plan.
    • Click on the “Change Plan Settings” link, then click “change advanced power settings”.  This window is where the real control over the power plan exists.

    • Browse through each item provided, and set power management to either disabled, maximum performance, or off, depending on the item. Things like turning off the hard drives are a bad idea on an acquisition system, as this can cause problems with long term timelapse.
    • One key item is the PCI link state power management. This should be set to “Off”. This item selectively disables power to the PCI bus. Some of the cameras and devices used in acquisition systems rely on PCI / PciE based cards to operate, and cutting power to these cards can cause all sorts of havoc.

    • Another common problem, probably the biggest I’ve seen, is the USB suspend entry. Again this function turns off the USB bus when not in use. This has caused crashes in software when operating USB devices, so it should be set to “Disabled”.

    • Once you’ve investigated each item and made any desired changes, click OK, and then close out of the power option windows.

    Making the changes noted above should make a big impact on the stability of your imaging system. Hopefully this guide helps you to avoid acquisition crashes on your system!

    -Austin

  • Photometrics LVDS cards on Win7

    I recently slogged through a tough install with a customer (Thanks Sean!!) in an attempt to run an older Photometrics camera using a PCI card in windows 7/xp. What we found was that the latest driver, (as of this post v. 2,7,10) is not working with PVDS cards! The solution for now is to roll back one version earlier, then things should be OK.

    You can basically tell if you’ll be affected by looking at the cable attached to your camera. an LVDS cable looks like this:

    LVDS Connector

     

    – Austin

     

     

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