Macroscope: Difference between revisions

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=== 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]
* 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]
* 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]
=== 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
* [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 ===
=== plate registration ===
* [https://store.caliperls.com/node/38774 ???]
* [https://store.caliperls.com/node/38774 this it???]
=== software (link to canon SDK req; starlight express drivers, switch&sense) ===
* [http://www.amazon.com/LightPad-A920-6x9-Light-Box/dp/B003N4ARIA/ LightPad A920 6x9 Light Box] 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 ....(link)
* Filter wheel software .... (link)
 
=== etc ===
=== etc ===


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=== 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 ==
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* sample images?




Revision as of 11:36, 20 December 2011

In the beginning, there was Disco!

coming soon ...


Macroscope:

what

why

capabilites (current and potential)

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...

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

  * CFP
  * GFP
  * YFP
  * mCherry
  * White
  • 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

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

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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