Chicago LSM - Product Announcement

early release screnshot

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Chicago Laser Scanning Microscope Controller, aka CLSM, was a software I created for a confocal microscope under $2000. I started it in an apartment in Bridgeport, Chicago with a friend, while we were finishing up our PhD research.

A prototype system was built, image acquired, confocal effect shown. So, technically, it all worked. But that was about it. Other priorities in life got us and the project had been left on the shelf for ten years. 

Recently, an opportunity came, and here we are. Add experiences after ten more years on scanning electron microscope, mass spectrometer, analog electronics and instrumentation software programming, the original software has now been re-written into a commercial grade controller software that can drive varies types of laser scanning microscopes platform, including but not limited to:

  1. Confocal Fluorescence Laser Scanning Microscope
  2. Multiphoton Fluorescence Microscope
  3. Second Harmonic Generation Microscope
  4. Scanning Electron Microscope (hypothetically)

Here are some features and specialties of CLSM. 

  1. Clock synchronized to external clock, such as ultrafast laser. 
  2. Up to four channels simultaneous acquisition.
  3. Up to 32Megapixel per image.  
  4. RESTful web interface for integration with other systems.
  5. 14-bit spatial resolution across field of view. 
  6. 14-bit hardware video resolution, extending to 16-bit with built-in averaging/integration functionality.
  7. Averaging based on pixel-by-pixel, line-by-line, or image-by-image. 
  8. Automatic oversampling on the scanner control signal to the smoothest scanning. 
  9. Mathematically complete 2D linear space distortion correction, aka Affine Transform. Directly generate perfectly geometry corrected image in linear space, include full support of scale, rotation, shear and shift correction. 
  10. Unidirectional and serpentine scan are both supported. 
  11. Flexible individualized latency settings for scanner, video chain, shutter opening and closing. 
  12. Built-in low level diagnostic tools.
    1. FFT 
    2. Smoothing algorithm for cleanest looking FFT plot
    3. Cumulative Noise Amplitude Spectrum, forward and backward
    4. (planned)Allan Variation for determine the best dwell time 
  13. (planned) Automatic calibration of linear space geometry correction 
  14. Memory leak tested for extended long period operation. 
  15. Pixel dwell time as low as 10ns for hypothetical controlling of scanning electron microscope. 

Hardware and Software Requirement:

  1. Analog Discovery Pro 3450 or similar, via USB or Ethernet
  2. OS support cover Windows 7 to 11 on 32-bit and 64-bit x86-64 PCs. Linux and Mac OS version can be provided upon special request. 
  3. National Instrument LabVIEW Runtime Engine (no cost)

Contact us at for pricing, licensing, evaluation, customization, and technology transfer.

We also provide simulation build for free evaluation. Full Affine transform and many other advanced features are supported in simulation build.