SLR cameras for Microscopy

Camera on Leica Microscope

Most of the time, I work with people who need measurable and accurate (quantitative) results from the images they obtain. While this constitutes the bulk of my daily job, there is a much larger group of people using cameras on microscopes for photomicrography. Or put simply -- taking a picture of what you see through the scope for the

purposes of presentation or archiving.These people live in an a space completely underserved by the microscope imaging community. Here’s why:

  • C-Mount cameras are usually cooled (which isn’t needed for basic trnasmitted image capture)
  • C-Mount cameras are usually specified to be linear and quantitative (again unneeded for basic image capture)
  • The software used by these cameras has more features than are needed to snap an image
  • The production rates for these cameras and cost of scale equal an unjustified high price for basic image capture.

Now when I use the term C-Mount camera I’m referring to cameras that are dedicated for microscopy use, which have no glass lens assembly in front of them, and connect to the scope using an ISO C-Mmount.

So what options are available besides the traditional camera? Enter the venerable SLR. Before the digital camera era, everyone had a film body camera on their microscope if they were acquiring images. This system could produce beautiful images, but required all the usual steps in film photography. There are a wide array of mounts available for cameras such as these, as most miroscope optical systems were designed to work with SLR cameras at some level.

Today there are a wide array of DSLR (Digital Single Lens Reflex) cameras available. These cameras use similar (but not exactly the same) optical setups that will, in most cases, work quite well on a microscope. Why is this?

  • In general, we don’t want glass to be in front of the sensor. DSLR cameras, like C mount cameras, use a lens connection, allowing for the lens to be removed, and the camera to be placed on the microscope. So the microscope becomes the “lens”.
  • Modern DSLR cameras like the D90 from Nikon or the 50D from Canon include a “live view” function. This function allows the user to view the live image from either the camera body, or the method I recommend, through remote control software running on a computer.
  • DSLR cameras include incredibly powerful image processors in-camera. This means you won’t ahve to fiddle as much with white balance to get a high quality image that accurately depicts what you see under the scope. Pathologists are famous for seeing these color balance errors as they have the best trained eyes when it comes to minute color change on stained specimens.
  • Unlike film or digital still cameras, newer DSLR cameras can acquire HD live video. Here’s an example from a Nikon camera. One can imagine the use of this for live microscopy recording, all with the same camera…

So why not use any handheld camera? Because the typical lower cost camera will not allow you to remove the lens assembly. This is the primary benefiet of DSLR and C mount systems.

If you’ve read this far and are interested in using a DSLR for your microscope, you’ll need a short shopping list of components on order to make everything properly work. Here are the components you’ll need:

  1. Camera Body (you don’t have to buy the camera with a lens if this will be a dedicated scope camera)
  2. Camera -> Microscope Mount system.
    1. You can use either a microscope manufacturer’s recommended system like the ones described here (Nikon F Mount options)
    2. Or use a high quality aftermarket adapter from a company like this (Canon and Nikon F Mount coupler)
  3. Control Software for your camera (Nikon uses software that you have to buy separately, canon software is included with the camera).

Notes on Acquisition:

Once you have the parts together, you’ll need to set the camera up for the right shooting mode. On most cameras you’ll see an “M” mode. This is preferred for microscope use. M is full manual mode. There is no focus or aperture for the camera to control on the microscope, so those adjustments are not required. The remaining adjustments (exposure time and ISO) can be controlled manually. For low light fluorescent work, use high ISO. For normal transmitted light, use low ISO. You can use the metering system on the camera to determine the exposure time, and all of these settings can be controlled from the computer. Finally, make sure to enable “exposure delay” mode, which will avoid capturing any vibrations introduced into the scope when the shutter drops open!

As always if you have any questions on this technique you can contact me with questions!

- Austin

Running Micro-Manager with a Nikon TI Microscope

If you are running uManager you will need to install the Nikon Ti Drivers, as well as have a way of configuring the scope settings. You can address both issues by installing Ti Tools. You can find the most current version of Ti Tools from Nikon’s Website (including 32 or 64 bit versions) here.

-Austin

Mobile Support!

I’ve Added a mobile support plugin to the website for those of you living on the road. It’ll work with almost every smartphone/iphone/droid type of device out there. Hope you like it!

Thanks to Alex King for the awesome free plugin!!!

- Austin

Steve Jobs Explains Back Thinned Chips!

A few of my work colleagues pointed out the well presented positive aspects of larger pixel, back thinned sensors. If anyone has heard me prattle on about this they’ll find it familiar! Fast forward to minute 1:00 for the points on the new iPhone 4 camera. Steve’s explanation is dead on!

- Austin

Split XY multipoints macro

Has been added to the free macros list under Macros & Journals!

Elements ND File Size Calculator

This is a calculator that will look at an ND experiment and tell you how large the resulting ND file will be. This is approximate and keep in mind if you are using the “save to TIFF” function the total size will likely be larger, due to the metadata saved per image in the tiff format.

Download Here

- I’ve added this to the free macros list also.

Austin

How to Set Large Icons in Elements

This is useful for large screens that are using very high resolutions. Sometimes the icons are so small as to be hard to click and unreadable.

Open Elements and select the View Menu, then Layout, then open the “Layout Manager”.

ToolbarButton_001

Next select the “Toolbar” Section on the Left (Step 1), then Select the “Large Icons” Checkbox on the right (Step 2). Finally to set this as the default option for all modes right-click the Toolbar icon and select “Apply to All”. Finally save the setting to a file “Step 3″. You should now have large icons!

ToolbarButton_002

- Austin

NIS Elements Stereo Zoom Settings

The Auto-calibration feature in Elements (beginning in version 3.1) is a great thing to have. You simply choose the objective you are working with, the software knows what camera you are running, so the calibration is calculated for you when you add the objective list.

While this is great for the compound scope systems out there, it’s not helpful for a variable-zooming stereo or macro system. Low and behold there is a nice feature in Elements to handle this, and here’s how it works:

The feature is called “Zoom Configuration” and can be found under the “Devices” menu.

elements location

To use this feature you’ll need to have at least one objective declared under the Calibration menu ->objectives list.

When you open the window you’ll see a configuration screen for the zoom optics. Configure as follows:

zoom2

Also – If you want the Zoom to appear in the live window you’ll need to check the “Zoom is located in the camera light path” checkbox.

With this complete you can close the config window. You’ll see a new tool available on the toolbar which allows you to enter the zoom value before acquiring an image:

zoom3

Note that for this to work you’ll need to have selected the main objective as active before you’ll see a calibration value in your acquired image.

This is an extremely useful tool and one I’m glad to see is available in Elements D up to AR!

- Austin

Micro-Manager 1.3 and Velleman Boards

If you are running micro manager and need to control a device via TTL or voltage, there is a nice driver written for umanager along with an inexpensive A/D card. The Card I used for a recent project was the Velleman K-8061. I’ve written up a simple how-to on connecting the board to a windows PC and getting umanager to run it.

Setup instructions for the Velleman Board and uManager 1.3

uManager Wiki on the K-8061 board

Velleman Board Link

-Austin

Bio-X Course Follow-up

Thanks to everyone who attended my first course on image processing (and acquisition as it turns out). As promised here are some links:

- MBF Tools for ImageJ. This is a suite of processing and analysis tools, provided by the McMaster Biophotonics Facility, which can be used for, among other things, splitting apart pigment based IHC specimen images.

***One of the course attendees asked how to merge multiple channels, without using primary color (RGB) values. For instance one may want to select “Red, Cyan and Green”. This function is available using the MBF Tools function found under Plug-Ins, then under the “Colour Functions” and finally using the “Colour Merge” command.

- This tool only merges two channels. It is possible to run this multiple times, so a merge can have a third channel added to it, and so-on.

- LOCI Formats Importer/Exporter is a tool which can be used to read and write many file types. It can also import metadata from many of the proprietary file types used today.

- I was not able to find a dynamic and interactive particle counting plugin for ImageJ, however when you have produced a count by selecting “Analyze particles” you can select the “Distribution” command from the Analyze menu to produce histogram distributions for every measurement type selected.

Please contact me if you have any other items you’d like me to cover. Thanks again!

- Austin