Austin's Imaging Blog

If you are enrolled for the Bio-X Image Processing and Analysis Workshop, I want to make sure you get the most from the course. To that end:

• If you don’t have a laptop please find someone to work with during the course, so you can follow along. Most of the subject matter is better absorbed if you have an opportunity to try it yourself.
• Review the subject matter as soon as possible after the course. The more images you work with and the more techniques you try the better understanding you will have of the various tools available.
• During the course if you have a question or area of interest that is not addressed please contact me via email, so I can address it.

- Austin

When using the “Wellplate2″ Macro with NIS AR you may have noticed a small but important limitation: Once you’ve loaded your specified sites into the 6D experiment, you can no longer make adjustments to the scope PFS offset. This means that for each experiment you run you either need the offset to stay the same, or you need to reload the sites into the ND window. I’ve made a simple workaround for this.

By running a small macro we can turn on the PFS, move the offset to a pre-determined value (that is defined by the user before running the experiment) and then disable the PFS while moving to the next plate.Here’s a walk through on how to set the macro up and on a description of the problem:

Problem: Note that the PFS values are off while I add sites to the experiment:

When I now enable to PFS the default values (0) are active. While this is not the case if I send the sites with the PFS on, I still cannot alter the sites in future experiments.

So when you install the macro (which can be found at the end of this post) you’ll need to set the macro up so that it runs each time elements loads. To do this go to the options menu and add the macro. Then set it as a “Start-Up” macro as shown here -

With that done we can restart elements and this will run the macro code.

Next we add the calls needed to the experiment to operate the macro. Your XY experiment window should look as follows in the “Advanced” section:

Finally we need to enter the value for the PFS offset. To do this select Macro menu, then Command, and choose the “Interpreted” command group. You should see three entries at minimum, one called “PFS_define_offset(). Run this command and enter the offset value you need for your experiment.

That’s it! Now each time your stage is moved to a new position this macro will override the PFS entered into the XY list and will set the value you specified in the step above. For ease of use the command above can be added to a menu entry or a button (using the layouts) if needed.

You can find the macro HERE.

-Austin

Here is the latest build for Elements if you are running a Lumenera camera. Follow the directions explicitly if you plan on updating or installing without a local rep available!

Download

I’ve added some PC spec sheets for each of the computer configs we sell. A few notes:

1. These show a monitor on them but this specific monitor is NOT INCLUDED.

2. The systems come with Windows XP SP3 (Which we will stay with until our major imaging apps support Windows 7).

3. System specs are subject to change at any time – check with your local rep or myself for current specs!

This is an interesting method of delivering biomolecules into living cells.

SEM image of Cell on Needlebed

http://www.technologyreview.com/biomedicine/24347/

Happy New Year!

Laura Sysko from Nikon sent us a How-To on outputting live graphs that can be included with a timelapse or other ND file. You can find the How To Here.

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Here’s to a merry christmas and a happy new year!

Details on the agreement between Nikon and UCSF for SIM can be found Here.

Nikon dropped big news at ASCB when they announced the development of two new super resolution microscopes. Two different technologies were announced, STORM and SIM.

The SIM technique was developed by Dr. Mats Gustaffsen, Dr. John Sedat and Dr. David Agard at UCSF. The technology doubles the XY resolution of a traditional CLSM, using a structured illuminations technique and custom manufacturing process. This method also supports 3-D sectioning as well as TIRF.

The STORM system was developed by Dr. Xiaowei Zhuang at Harvard University. This system uses statistical sampling of multiple exposures to produce extremely high resolution images. It supports 3-D image construction as well.

At the show floor Nikon had the A1R-MP Confocal system running. This system can perform very high frame rate acquisitions using multiphoton excitation.

Key features are:

• 420 fps with MP excitation
• Simple switching between resonant and non descanned detector systems. (done on the fly with no need to change hardware)
• Can be coupled with Plan Apo Water Immersion IR 60x lens

Hamamatsu has released a dual chip camera for ratiometric applications. The camera includes 2 of the ER-150 CCD’s, with one chip supporting discreet focusing, which allows the system to be chromatically aligned. Key features of this system are:

• Electronically linked filter cubes that auto-configure the camera for use.
• Independent focusing between CCD’s, X/Y translation is automatically performed by the camera.
• Competitive price at $33,000.

D2 Camera