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In the beginning, there was [[Disco!|http://youtu.be/8ErHEaAgK3Q]]
In the beginning, there was [http://youtu.be/8ErHEaAgK3Q 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: ==
 
=== parts list and sources ===
=== basic structure ===
=== 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 [http://usa.canon.com/cusa/consumer/standard_display/sdk_homepage SDK] can be requested [http://consumer.usa.canon.com/cusa/support/consumer/eos_slr_camera_systems/eos_digital_slr_cameras/digital_rebel_xt?fileURL=ps_sdk_form&pageKeyCode=downloadLicense&id=0901e02480057a74_1&productOverviewCid=0901e0248003ce28&keycode=Sdk_Lic here].
 
=== LED illumination packages. filters and leds - chroma...clearance...mention gel filters... ===
* [http://www.amazon.com/Professional-Mini-Ball-Camera-Mount/dp/B000L47AHG/ref=pd_cp_p_0 Ball & Socket heads] for aiming LEDs.
 
* LED lenses
  * [http://www.luxeonstar.com/Carclo-27-Deg-Frosted-Tri-Lens-With-Holder-p/10508.htm Wide dispersion]
  * [http://www.luxeonstar.com/Carclo-22-Deg-Frosted-Tri-Lens-With-Holder-p/10511.htm Medium dispersion]
  * [http://www.luxeonstar.com/Carclo-18-Deg-Tri-Lens-With-Holder-p/10507.htm Narrow dispersion] used for fluo illumination.
* [http://www.amazon.com/Instant-External-Diffuser-Cameras-Tripod/dp/B005K1XX58/ White LED diffusion boxes]
* [http://www.ledsupply.com/03021-d-e-700.php 3021-D-E-700mA BuckPuck LED driver] and [http://www.luxeonstar.com/Harness-for-E-or-I-Drivers-6-Wire-With-Pot-p/3021hep.htm wiring harness]
* Single Luxeon LED lens for BFP
 
* LEDs
  * [http://www.luxeonstar.com/Royal-Blue-447-5-nm-20mm-Tri-Star-Rebel-p/mr-r0500-20t.htm CFP]
  * [http://www.luxeonstar.com/Blue-470nm-20mm-Tri-Star-Rebel-174-lm-p/mr-b0030-20t.htm GFP]
  * [http://www.luxeonstar.com/Cyan-505-nm-20mm-Tri-Star-Rebel-390-lm-p/mr-e0070-20t.htm YFP]
  * [http://www.luxeonstar.com/Amber-591-nm-20mm-Tri-Star-Rebel-396-lm-p/mr-l0000-20t.htm mCherry]
  * [http://www.luxeonstar.com/Neutral-White-4100K-20mm-Tri-Star-Rebel-540-lm-p/mr-wn100-20t.htm White]
  * [http://www.superbrightleds.com/moreinfo/component-leds/prolight-1-watt-ultraviolet-leds-140-degree-viewing-angle/334/ BFP]
 
* Excitation filters. Chroma clearance bin as possible.
  * CFP: Chroma D436/20x 25mm
  * GFP: Chroma [http://www.chroma.com/products/part/771 S470/40x 25mm]
  * YFP: HQ500/20x 25mm
  * mCherry: Chroma [http://www.chroma.com/products/part/1135 ET572/35x 25mm]
  * BFP : Chroma [http://www.chroma.com/product/individual-filters-mirrors/widefield-microscopy/D395_x_40x-EX 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.)
 
* [http://www.optcorp.com/product.aspx?pid=354-1630-1632-13255 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 ===
* [http://www.mccdaq.com/usb-data-acquisition/SwitchAndSense-8-8.aspx Measurement Computing Switch and Sense 8/8] Overdoing it, but very plug and play
=== plate registration ===
* [https://store.caliperls.com/node/38774 this it???]
* [http://www.amazon.com/LightPad-A920-6x9-Light-Box/dp/B003N4ARIA/ 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) ===
* [http://www.mccdaq.com/usb-data-acquisition/SwitchAndSense-8-8.aspx Switch and Sense]
* [http://usa.canon.com/cusa/consumer/standard_display/sdk_homepage Canon SDKs] are requested [http://consumer.usa.canon.com/cusa/support/consumer/eos_slr_camera_systems/eos_digital_slr_cameras/digital_rebel_xt?fileURL=ps_sdk_form&pageKeyCode=downloadLicense&id=0901e02480057a74_1&productOverviewCid=0901e0248003ce28&keycode=Sdk_Lic here].
* Macroscope operating software ....(Binary, Source links)
* Filter wheel software .... (link)
 
=== etc ===
 
== 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 ==
* [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0015179 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]
* [http://www.google.com/url?sa=t&rct=j&q=worm%20breeders%20gazette%20fluorescence&source=web&cd=2&sqi=2&ved=0CCwQFjAB&url=http%3A%2F%2Fwww.wormbook.org%2Fwbg%2Farticles%2Fvolume-18-number-1%2Fusing-leds-as-a-low-cost-source-to-detect-gfp-and-dsred-2%2F&ei=9DriTqWELsXn0QGq8KDvBQ&usg=AFQjCNHTk8rKx83V0hK8FYfsyvIQtcDh7w&cad=rja ? 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?
 
 
 
[[Image:Macroscope frame 1 dimensioned.png|400px]]
[[Image:Macroscope cam-fw-lamps 1 back.jpg|400px]]
[[Image:Macroscope cam-fw-lamps 1 low.jpg|400px]]
[[Image:Macroscope cam-fw-lamps 1 side.jpg|400px]]
[[Image:Macroscope camera mount detail 1.jpg|400px]]
[[Image:Macroscope camera mount detail 2.jpg|400px]]
[[Image:Macroscope entire 1.jpg|400px]]
[[Image:Macroscope entire 2.jpg|400px]]
[[Image:Macroscope entire high.jpg|400px]]
[[Image:Macroscope fluo lamps 1.jpg|400px]]
[[Image:Macroscope fluo lamps 2.jpg|400px]]
[[Image:Macroscope fw 1 low.jpg|400px]]
[[Image:Macroscope fw apart 1.jpg|400px]]
[[Image:Macroscope fw apart 2.jpg|400px]]
[[Image:Macroscope fw apart 3.jpg|400px]]
[[Image:Macroscope fw coupler detail 1.jpg|400px]]
[[Image:Macroscope fw coupler detail 2 bottom.jpg|400px]]
[[Image:Macroscope fw coupler detail 2 top.jpg|400px]]
[[Image:Macroscope fw coupler detail 3.jpg|400px]]
[[Image:Macroscope fw coupler detail 4.jpg|400px]]
[[Image:Macroscope fw coupling 1 high.jpg|400px]]
[[Image:Macroscope fw coupling 1 med .jpg|400px]]

Latest revision as of 08:30, 30 January 2017

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:

parts list and sources

basic structure

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...

  • LED lenses
  * Wide dispersion
  * Medium dispersion 
  * Narrow dispersion used for fluo illumination.

* 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.)

control box

plate registration

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

etc

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


  • sample images?


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