Macroscope: Difference between revisions
From OpenWetWare
Jump to navigationJump to search
No edit summary |
Rotem Gross (talk | contribs) |
||
(8 intermediate revisions by 3 users not shown) | |||
Line 6: | Line 6: | ||
== Macroscope: == | == 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: == | == 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 === | ||
=== | * [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 == | == 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? | |||
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...
- Ball & Socket heads for aiming LEDs.
- 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.)
- 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)
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
- 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?