Macroscope: Difference between revisions

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== Macroscope: ==
== Macroscope: ==


=== what ===
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.
=== why ===
 
=== capabilites (current and potential) ===
Credit:
Remy Chait, Michael Baym
Kishony Lab, Harvard Medical School


== To build: ==
== To build: ==
Line 15: Line 17:
=== basic structure ===
=== basic structure ===
=== custom parts (cam and filter mounts) ===
=== 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 ===
=== camera ===
=== filters and leds - chroma...clearance...mention gel filters... ===
* 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 ===
=== control box ===
=== software (link to canon SDK req; starlight express drivers, switch&sense) ===
* [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 ===
=== etc ===


Line 25: Line 79:
=== notes ===
=== notes ===
* Fluorescence shading correction. Divide images by a flat field standard
* 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 ===
=== improvements ===
* Better darkfield illumination
* Better darkfield illumination
* 3D imaging of fluorescence in transparent volumes using sheet illumination (laser, cylindrical lens, )
* 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]




== 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
* sample images?
* ? 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




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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