Macroscope

In the beginning, there was Disco!

coming soon ...

Macroscope:

The Macroscope is a device for fluorescence imaging at macro-scale. It was designed to image colonies and lawns of fluorescent bacteria growing on agar plates [Ref 1], but could be used for multiple other applications in biology and engineering.

Credit: Remy Chait, Michael Baym Kishony Lab, Harvard Medical School

To build:

custom parts (cam and filter mounts)

• Filter wheel mount. McMaster-Carr part *** machined to this spec ^^^. This part can also be ordered directly from emachine shop. Requires mating to the adapter that comes with the filter wheel (picture links).
• Camera mount. McMaster-Carr part *** drilled with 1/4" bit to allow mating to camera tripod mount.
• LED filter coupler. 1 per LED. Available through eMachine Shop. design link.
• LED mount and heat sink. 1 per LED. Available through eMachine Shop. design link.

camera

• Canon T3i, with Canon EF-S 60mm f/2.8 Macro USM Lens, and Canon ACK-E8 AC Adapter Kit for Rebel T2i
• Canon SDK can be requested here.

LED illumination packages. filters and leds - chroma...clearance...mention gel filters...

• Ball & Socket heads for aiming LEDs.

• LED lenses

  * Wide dispersion
  * Medium dispersion 
  * Narrow dispersion used for fluo illumination.

• White LED diffusion boxes
• 3021-D-E-700mA BuckPuck LED driver and wiring harness

* Single Luxeon LED lens for BFP

• LEDs

  * CFP
  * GFP
  * YFP
  * mCherry
  * White
  * BFP

• Excitation filters. Chroma clearance bin as possible.

  * CFP: Chroma D436/20x 25mm
  * GFP: Chroma S470/40x 25mm
  * YFP: HQ500/20x 25mm
  * mCherry: Chroma ET572/35x 25mm
  * BFP : Chroma D395/40 25mm

Emission filters and automated filter wheel

• Emission filters. Chroma clearance bin as possible (50mm filters = $$)

  * CFP: Chroma D480/40m-50mmr
  * GFP: Chroma D530/20  50mm
  * YFP: Shares GFP emission filter
  * mCherry: HQ645/75m 50mm
  * BFP: Chroma 460/40 55mm (oops, should have been 50.  Works anyway, not perfectly.)

• Starlight Xpress USB 5 Position 2" Filter Wheel - 72mm Male Input/ Output. Make sure here to get a filter wheel insert that is for unthreaded filters!

control box

• Measurement Computing Switch and Sense 8/8 Overdoing it, but very plug and play

plate registration

• this it???
• LightPad A920 6x9 Light Box for transmission imaging.
• Hey! - Include modifications to registration plate and light box(pins) for transmission imaging.

Software (link to canon SDK req; starlight express drivers, switch&sense)

• Switch and Sense
• Canon SDKs are requested here.
• Macroscope operating software ....(Binary, Source links)
• Filter wheel software .... (link)

Thoughts:

notes

• Fluorescence shading correction. Divide images by a flat field standard
• Filters. Interference filters are far and away the most costly part of this device, but have an enormous impact on signal to noise ratio. A very inexpensive but lower S/N filter option is to use theatric gel filters, available with transmission spectra from RoscoLUX, ... (ref worm breeders). A still cheaper option is to see how much fluorescent signal can be extracted using just the RGB filtered channels of the cameras sensor, along
• Often, grabbing a single channel of the output fluorescent image (eg, Blue for CFP emission) further cuts some background and may improve the signal for certain fluors.

improvements

• Better darkfield illumination
• 3D imaging of fluorescence in transparent volumes using sheet illumination (laser, cylindrical lens, )
• Hyperspectral imaging to allow fluorescent compound identification and spectral unmixing of combinations of FPs, and for transmission spectroscopy...(ref)

Similar Tech

• Chait R, Shrestha S, Shah AK, Michel J-B, Kishony R (2010) A Differential Drug Screen for Compounds That Select Against Antibiotic Resistance. PLoS ONE 5(12): e15179. doi:10.1371/journal.pone.0015179
• ? Ian Chin-Sang1 and Weiwei Zhong Using LEDs as a low-cost source to detect GFP and DsRED Worm Breeder's Gazette, Department of Biology, Queen’s University, Kingston, ON, Canada, 2Department of Biochemistry and Cell Biology, Rice University, Houston TX

• sample images?