Andor sCMOS

This is a quick post - things are busy! Andor has a white paper and information up on a new "Scientific CMOS" sensor. Have they overcome the limitations to CMOS sensors for Scientific applications? This could really change the landscape for microscopy imaging!


- Austin

Why do I want a low resolution camera?

These days it's not uncommon to hear about consumer cameras with 10+ megapixel resolution. To the average consumer this seems like a good thing. How can more pixels be anything but good, right? In reality there are several tradeoffs to using more pixels. This is especially true for any scientific imaging (this really applies to low light an/or quantitative imaging such as microscopy and astronomy). So what are the downsides?

First let's look at the concept of a pixel. Pixels are physically sized on a CCD or CMOS sensor. For an example of pixel architecture check out this page. The physical size of a pixel affects several aspects of image acquisition:

1. Dynamic Range
   
2. Sensitivity
3. Resolution
4. Speed

Most people simply think "bigger pixels means less resolution" or "more pixels result in more resolution". This isn't the only thing that is affected by pixel size. A more interesting question to ask would be "What am I sacrificing by using smaller pixels?". Of the four performance aspects above three are negatively impacted when using smaller pixels. These are:

1. Dynamic Range
2. Sensitivity
3. Speed

Dynamic Range

The dynamic range of a sensor is first determined by the full well capacity(FWC) of a single pixel. This is a measurement of how much energy the pixel can hold before either becoming nonlinear or before the energy spills out of the pixel into neighboring pixels (called blooming). Smaller pixels simply cannot hold more energy due to physical size, so smaller pixels = less dynamic range. Let's compare two common chips - the Sony ICX-205AL CCD, used in the Photometrics CoolSNAP cf2 camera (and many others), with the Sony ICX-285 CCD, used in the Photometrics CoolSNAP HQ2 (this ccd is the most prevalent in modern microscopy cameras).

• The 205 CCD shows a FWC of 9,700 electrons.
  
• The 285 CCD shows a FWC of 16,000 electrons.
  
• Note that the 205 chip has a pixel size of 4.65um, while the 285 has a FWC of 6.45um.

In the case of these two sensors, a 2x increase in pixel area provided a 65% increase in FWC. The larger chip has more FWC, so I can detect a range of brightness with more accuracy, or have more range of bright to dark, or more dynamic range.

Sensitivity

This is an easy one: If I take a given area of my image being projected onto my chip, I chop that area (or that brightness value) up more times if I have smaller pixels. Lets assume I have one chip using 5x5um pixels, with another that uses 10x10um pixels. Let's also assume the light being projected onto the sensor area is 100 photons per 100um square area. Using my smaller pixel chip each pixel could collect 25 possible photons. Using my large pixel chip each pixel can collect 100 possible photons, so the larger pixel camera can grab more light per pixel than the small pixel camera.

Speed

The argument I make here isn't really a technolocal limitation but more a common product/market limitation. All of the cameras we use are set up to collect an image projected from a microscope into roughly a 1" diameter area. So I am limited in how much area I can use on my chip. Because of this if I have bigger pixels I cannot simply make a gigantic chip that has say 1000x1000pixels, as it's possible the corners of my chip won't have any light projected from my scope. This means that intrinsically I'll either find chips with a lot of small pixels, or chips with fewer large pixels.

When considering speed there are several factors: exposure time, analog to digital conversion time, and "frame shift" time. (I'm using this term to conver interline shift and FT operations for those purists out there). Now if you look at any data sheet you'll notice there is some "top speed" a camera can go. You can bin the camera and use a small readout array but you hit a limit - why?

Let's assume we have a camera of 100x100 pixels that can expose an image and get enough light in 10ms. Let's also assume our A/D converter that turns electron values into digital numbers can operate at very high speeds, say 100Mhz. In a case like this our camera can theoretically run at 100 frames per second, which is quite fast. Now what aspect of the system will stop me from say driving the camera at 10,000 fps? If we consider that the camera must move each pixel's energy off of the chip, using shifts of energy from one pixel to another or into some series of registers, whatever time it takes to move from pixel to pixel will become important. This is referred to as the shift time or shift rate. Depending on the architecture of the camera this time will affect the camera to different degrees, but ultimately this is a measurement of "How fast can I move energy across my chip?". This bucket-brigade type of energy transfer is what takes a electron charge in pixel 1A, and spits it out the other end of the chip into the A/D converter.

So using our fake camera here let's say it takes our camera 50 microseconds to move from one pixel to another. Then let's consider how many moves must be made to get pixel 1,1 out the other end of the chip at position 100x100. Basically pixel 1,1 needs to be moved 100 pixels down and 100 pixels over. So 100x100=10,000. Each shift = 50us, so 50us*10,000 = 500,000us, or 500ms. So using our fancy super fast camera we can only go 2 frames per second!!!

Obviously the example above is using excessively show shift rates so I can make my point. The bottom line here is that shift times do have an impact. So how does this relate to big pixels? Well if I have bigger pixels we already found that I must use less of them. Less pixels = less shifting that needs to occur, so the impact of shift rates becomes less! Ultimately you'll find that cameras like a 128x128 EM system can go up to 4000 fps, whereas a 512x512 EM system only goes up to 500fps, with the difference being shift rate*pixel count.

Conclusions

So many times I am asked why big pixels could possibly be better. Now you know! Don't let the hype of "megapixels are cool" lead your lab into an inappropriate camera for your research. Remember that the camera is a detector, just like other instruments. While the appearance of the image may suffer with large pixels, the data contained in the image can be more informative and accurate than data collected using high resolution systems. Try to prioritize what performance aspects will aid your area of study, and keep these aspects in mind when finding the right camera for your work. You'll be happier in the end with the right tool for the job.

- Austin

Elements Downloads

You can find the latest builds of Elements Here:

NIS Elements AR or BR Build 548

NIS Elements D Build 548

Something Broken?

When a camera or a device isn't working there can be any number of things wrong. How do we narrow the potential list down? I've taken a page out of my Toyota service manual and made a basic diagnostic flow chart which one can follow. This chart will basically work with any device and any software. Just remember the "normal" arrangement of what it takes for software to run a device:

1. Control software that the user clicks to control device
2. Drivers that the software uses to talk to each device's driver (or serial / parallel ports)
3. Windows Drivers (if used with device)
   
4. Hardware used to talk to device (serial, usb, parallel or PCI Card)
5. Device Brains (firmware)
6. Device itself

If any one of the links in this chain is broken or missing the whole arrangement won't work. You can find the flowcharts which help identify the problem here.

How to use Object Count in Elements

This is from the Nikon marketing group - excellent work if you are new to object count!
Download PDF

Elements Build 548 Released

Yes this is a bit late. Things are busy these days!

Elements B 548 can be found here if you need to download it. As usual back up all of your optical configurations and take screen shots of any filter configurations (i.e. if you are using sutter wheels) just to be safe.

So far this build has been stable. Only one or two bugs discovered. The major addition I see is we can now run High Dynamic Range processing from within elements. I can see why this would be a major advantage for stereo systems, as well as fluorescent images where the signal differences can be large. Haven't tried it yet but it looks great.

Austin

Luminera Infinity 3-1 Review

Review of the Luminera Infinity 3-1

Up for review is a new Infinity 3-1 camera from Luminera. The camera is a new venture for Luminera as it uses a high grade monochrome Sony IXC-285 CCD. This is the same sensor used in many of the Photometrics CoolSNAP cameras, Hamamatsu ORCA cameras and many others. This is my first review, so comments on the formatting are encouraged!

What Comes with the Camera:

Luminera cameras are all shipped in the same packaging. A cardboard box with foam inserts. Included in the box are:

- Camera itself

- USB cable to connect the camera

- Software on CD

- Documentation

Installation and Setup

Installation of the software was a snap. After installing the CD and following the on screen prompts the CD installed the software for operation and the camera drivers. Once that was complete I plugged the camera in and it identified in windows correctly. The usual WHQL driver warning popped up.

Image Quality

The system uses an “analog” type gain slider, so no true ADU analysis was possible. The following measurements were performed with the Gain set to 1.02:

- Read Noise = 49 Counts

- Dark Current @ 4.5 Sec = 261 Counts or 58 counts per second

- Frame Rate = ~15fps (unable to measure sequence timestamp in software)

- The camera read out “0” count values regardless of setting the gain to maximum and exposing for 4.5 seconds. (Bias offset incorrect)

- Gain control appeared non-linear. Images were acquired with no light to the camera, with gain changes from ~1 to ~11. Results are graphed below.

Conclusions

This is a great low cost solution for less than bright fluorescence when used for non-quantitative imaging. In order for the system to be a truly quantitative unit the bias must produce no “0” count values for each gain state used. Ideally some data would be provided with the camera showing the Electron to ADU conversion factor for each gain state used. These negatives aren’t really bad per se’. Considering the market space Luminera targets this camera should fit the needs for higher sensitivity, good performance across the normal fluorescence wavelengths, small size and simple operation. On top of all that this is the

best-priced camera that uses the venerable Sony ICX-285 CCD.

-Austin