Saturday, September 12, 2009

I've Moved!

I've moved my blog site to my homepage at

To get to the site use this link or enter in your web browser.


Tuesday, September 8, 2009

DXM-1200 C Camera Compatibility

A few years back Nikon released a very cool 12 megapixel stepping camera, called the DXM-1200C. The camera was reliable and a nice product for many years. Unfortunately the march of progress made a dent in this camera. The system, like many others, relied upon a proprietary PCI card for transfer of image data to the PC. This reliance required that the PCI card was happy living inside whatever computer the customer had.

As time continued the card moved from the "most current" to not functioning with newer chipsets. As problems begain to appear with the chipsets more and more people found that they would buy a nice new computer for their imaging system, only to discover the camera would not work with it! In an effort to reduce lost time Nikon produced a document describing which chipsets are known to work and which were known not to work. Hopefully this doc will help a few of my customers avoid this issue! You can find the doc here.

Tuesday, August 25, 2009

Video of Human Blood Clotting

I Found this while searching for a fluorophore. Very cool to watch on youtube!!

Human Blood Clotting

- Austin

Monday, August 24, 2009

Sensor Size reference Chart

Recently a colleague sent me a link to sensor sizes. Many of these are for consumer cameras, however the general references (1/3', 2/3" and so on) are helpful for microscopy cameras.

- Austin

Tuesday, June 23, 2009

Pulse Control within NIS Elements 6-D Acquision

These directions will allow user control over an optical configuration to be specified at a given time-loop inside of the define/run experiment. So for instance if one wanted to trigger a shutter or light source to flash un-cage at the beginning of a high-speed acquisition, this would meet the need. These are a bit lengthy but remember the setup is only needed once!

  1. Create an optical configuration that activates your pulse. You only need the configuration to be active, but note the shutter should be set to “active shutter” and CLOSED when the optical config is selected. The shutter should be set to open only when the user presses the shutter button or when the camera is acquiring.
  2. Download my macro file that contains the control code needed for this to work. (If you have Quicktime installed windows will think this is a movie - make sure to Right-Click on the link and select "Save Target As". )
  3. Save the above macro into something like c:\Macros\ or wherever you can easily access it.
  4. In Elements select the Macro Menu, then "Open Macro" and open the macro file.
  5. Note in the macro file the lines that read "Stg_SetShutterState(3,1); this means "set the state of a selected shutter type(shutter type,Open)" . So set the first number to the shutter you want to control. (0=EPI, 1=DIA, 2=Aux1, 3=Aux2). The second number is easier - 1=open and 0=closed. ALL YOU NEED TO DO is make sure you are controlling the correct shutter, by changing the first number in the 2 lines of code in the macro to drive the correct shutter!
  6. Note in the macro the "Wait(1.00); command. Where the 1.00 sits is the amount of time the shutter should remain open. For a pulse time of 500 milliseconds the code should read "Wait(0.500);
  7. Test the macro at this point by running it. The desired shutter should open, wait and close. if modifications need to be made to the optical config or the code now is the time to do it!
  8. Next set up a text experiment that has 2 different time phases at minimum. Click the "Advanced" button to show the advanced time controls.
  9. Set the "Advanced for" box to read "Time Phase 2"
  10. Select the check box that reads "Execute Command at the Beginning..."
  11. Click the Arrow on the right side of the entry box and select "run macro"
  12. Go find the macro file you downloaded and modified earlier and select that macro.
  13. Your configuration should now look something like this one:
  14. Set the acquisition rate you want in time phase 2.
  15. Back up the experiment using the Save button.
  16. When you run the macro, and you reach time phase 2 the pulse will occur at the same time as the second time phase, without interuppting the experiment flow.

- Austin

Friday, June 19, 2009

iPhone ResCalc Review

A few weeks ago I purchased an iphone. While browsing apps I found one that we can use in the research community! A company called Zem Dynamics (who also offers FRAP solutions for live cell imaging) has released a small app that can calculate minimum resolvable distance, as well as optimum camera pixel sizes for a number of objectives and magnifications.

Positive Notes

  • This takes a lot of time and energy out of finding the best camera for a given optical setup. It's also a good way to find out how much binning will affect a given input image and how far one can bin when using various magnifying tube lenses or c-mounts.
  • Simple operation and controls eliminates a lot of potential error.
  • The app sells for $1.99. At this price you can skip that cup of afternoon coffee and break even on owning the tool!
  • This app loaded and ran very quickly with no crashes. I ran it on an iPhone 3G-s.
  • Pressing the Info button on the app switches the view from resolution to field of view calculations. This is very helpful when determining how much area a given camera will collect, or to find the best match between a camera and magnifying lenses.

Negative Notes

  • Pressing on the output values (either the pixel size or the resolution) brings up the iphone keyboard. There is no way to hide the keyboard or complete an entry of pixel size, so the only way to hide the keyboard is to close the application.
  • I'd like to see additional numerical apertures to support more objectives (and other scopes like stereo's and macrozoom systems).

From my calculations this app is using the standard Nyquist criteria of (0.61*emission)/Numerical Aperture. I have contacted the manufacturer to discover the pixel size calculations, however it seems to be ~2.5 pixels per diffraction limit. This is a good compromise setting to use, (see my resolution calculations here).

Overall this is a well designed and very useful app. I'd suggest anyone using or working with microscopes or imaging systems will find this a helpful tool. Of course you'll also need to own an iphone to run it :-)

- Austin Blanco

Copying Elements Settings for Multiple users

After installing a new imaging system it's common to receive a phone call or email that goes like this, "The IT guys stopped by today and added our computer to our comany/university network. Now all of our settings are lost!". Why does this happen and what can be done?

All settings for elements are stored on a per-user basis. When a different user logs in (i.e. the user assigned from a company network vs. the default user that is installed on the PC) the software expects that user to want his or her own settings. Thus no settings are copied over. In the majority of cases this should NOT be the use case for a user group. In my experience almst everyone would like to start with the "default settings" and then modify them to their needs. For now there isn't a copy button available, so we need to manually copy the settings.

Getting Started:

Copying settings is actually a simple process if done correctly. A few notes on this:

  • When moving to a new domain or user, don't delete the old user until the new user setup is working well for you!
  • Make sure to copy the backup files we generate to a common directory. For instance don't save to the "desktop" when logged in as administrator, as non-admin accounts may not get access to the admin desktop, leaving you no way to snag the needed backup files. Instead copy the backup files into a folder like c:\Elements_settings.
Backing up:

We need to back up 3 items: Program menu/docker layouts, optical configurations and macro settings.

  1. With the program running and all devices connected, click the "explore optical configurations" button.
  2. There are two backup buttons here. First click the Backup button that sits between the optical configs and the camera/scope settings. Save the file to back up the settings. Secondly click the backup button below the objective list. Name this backup_objectives.
  3. Once these files are backed up we can close the optical configuration window. Next we will back up the menu layouts and docker settings. To do this select the View menu, then Layout, then Layout Manager.
  4. In the layout manager we will export the current layout to an xml file. ***because all of these files are *.xml be sure to name them descriptively so you can figure out which file is for what backup later.
  5. Next we will check up on our macros. In some installations macros may be configured to run every time elements starts. In these cases when users are switched these "start-up macros" will need to be re-specified. To check if you are running any startup macros, go to the Macro menu, then select Options. In the window on the left-hand side you'll see any macros that are set to load when elements starts, as well as whether those macros are activated as "start-up". See the example below where I have one macro set as a start-up macro.
  6. Make sure to find where this macro file sits on the computer so that we can add it into the new user account later. This can be found by viewing the "full path" info below the white macro box.
Copying Over

With the backup complete we can log out of the current user and log in to our new user. Once logged in as the new user launch Elements.
  1. Open the optical configurations window. Click the Restore button below the objectives list and load the objectives backup file.
  2. Click the restore button next to the optical configurations and load the optical config backup file you saved earlier.
  3. Select the View menu, then layouts, then layout manager. Click the "Import Layouts" button and select the layout file backed up earlier.
  4. If you had any startup macros selected, click the Macro menu, then Options. Add any macros needed and set them to startup if required.
  5. Test the system to make sure the previous user account settings have been transferred successfully.
Hopefully this guide will help users when needing to copy settings to new user accounts. There is nothing wrong with using the same three or four backup files and loading them into multiple user accounts as well! Please post here or email me if you'd like to see any additions or changes made to this entry.

Austin Blanco