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OPT part list


Vendor/ Part Number


Transmitted light source

White light bulb (eg IKEA SPARSAN low energy light bulb* [+ socket & wiring]) + diffuser (eg Thorlabs #DG20-600) + small metal block to serve as base for the diffuser glass.

We suggest a common round, wide-base light-bulb socket such as those commonly found in hardware stores for ceiling or wall fixtures. A desk lamp would work also!

To hold the diffuser glass upright we suggest a small metal block (eg 1x5x2cm) glued to the edge of the glass, as shown in the diagrams. The glossy side of the diffuser glass should face the sample, and the "rough" surface should face the light bulb.

* We have obtained a more even illuminating field with this cheap solution than with light sources such as those used for stereoscopes with halogen bulbs and condenser lenses!


Incident light source 


LED control:

 LuxeonStar blue LED (470nm) #MR-B0040-20S + condenser lens (LED optics) #FLP-N4-RE-HRF + heatsink #N25-20B (caution, these LEDs get extremely hot) +  Thorlabs #MF469-35 excitation filter (there is considerable bleedthrough of other wavelengths with blue LEDs so an excitation filter is necessary to prevent reflected spots superimposed on fluorescence images). Filter should be placed in front of the LED condenser lens (glued or taped). See detail of assembly in diagrams below.

Thorlabs mounting base #BA2/M + post holder #PH40MM + post TR40/M
(glue heatsink to tip of post)

Luxeonstar FlexBlock LED driver #A011-D-V-700 (control LED power) + 

Sparkfun #COM09939 20K Ohm potentiometer

For details on the wiring of LED electronics follow this link http://www.luxdrive.com/download/?dltf&dmid=1512 and follow a video with instructions for assembling the LED assembly and its operation here: http://www.youtube.com/watch?feature=player_embedded&v=PdC8MFuc5DI


++ +


15x30cm Breadboard + 30-45cm Rail (eg Thorlabs #MB2030/M + #RLA450M)

The rail and carrier hold the Infinitube+lens+camera and allows adjustment of working distance for different lenses. 

Alternatively, the whole setup can be assembled on a larger breadboard for better stability (eg Thorlabs #MB3060M).

Sample holder assembly

XYZ travel stage with 60mm travel in all directions. Can be assembled with 3x rack & pinion dovetail travel stages with 60mm travel (eg Edmund optics #55-021) + kinematic mount with stage plate (eg Thorlabs #KM100B) + custom made metal post (2x2x10cm) to hold XYZ travel stage assembly. The easiest way to connect the motor to the kinematic mount stage may be to simply glue it (eg Epoxy])!

Attention: The stage assembly should be well secured and connected to the breadboard otherwise it may tip, fall and destroy the sample chamber and spill BABB! Also, an improperly secured XYZ stage will introduce miss alignments which result in reconstruction artifacts. A tight connection between all parts is also essential to prevent acquisition miss alignments.

Stepper motor 400step (eg Sparkfun #ROB10846) + mounting hub (eg Sparkfun #ROB10006) + magnet disk (eg Sparkfun #COM-08890).

Attention: the Sparkfun stepper motor above requires an external power supply of 3V 1A, fed via easy driver (see below for more details)! Others may operate with 12v...check!


Motor control

 Arduino UNO +  Sparkfun Easy-driver stepper motor driver #ROB10267

For details on wiring the motor control (Arduino + easy driver) follow this link: http://www.schmalzhaus.com/EasyDriver/Examples/EasyDriverExamples.html

Attention: the Arduino and easy driver do NOT provide enough power to operate the stepper  so an external power supply is needed and is wired to the easy-driver as explained in link !


Sample chamber

5x5x5cm or 2.5x2.5x2.5cm optical-quality glass cuvette (eg Hellma #704.003OG or custom made [see diagrams for instructions on a DIY sample chamber). The sample block is held submerged in a mixture of BelzylAlcohol+Benzyl Benzoate (BABB) inside this chamber (=cuvette) while imaging. The cuvette needs to be "raised" 2-5cm (depending on its size) for the sample to be within the camera field of view. This can be done by adding feet to the couvettes or using blocks of any material resistant to BABB (avoid plastics or painted metal!); glass or bare metal blocks are OK. Another option is a mini lab jack (eg Thorlabs #L200 - expensive!).


Camera + detection optics

1x, 0.5x and/or 2x objectives and tube lens system (eg Infinity Infinitube standard #210200 +  Infinity IF-3 lens# 991102 [1x mag, 195mm WD] + Infinity filter holder #991152

Green fluorescence emission filter (eg Thorlabs #FEL0500)


Infinity mounting clamp #770170 + Thorlabs post #TR20/M + Thorlabs post-holder #PH2  (connects to rail carrier) + rail carrier #RC1


 Any c-mount CCD/CMOS camera which can be fully controlled by microManager, preferably 12 bit capable (not necessary). Larger/heavier cameras (eg cooled or EM-CCDs) may require a different camera+lens holder assembly than the one described above. Small form cameras (eg The Imaging Source or Thorlabs cameras) are light, don't require additional holders and remain in position simply attached to the lens tube.

If your camera is not fully supported by microManager and it has "trigger" input it will still be possible via an Arduino sketch to synchronize image acquisition with motor stepping.

 (IF3+filter holder+tube)+

A very simple Arduino sketch to run the OPenT can be downloaded below. This is useful if your camera is not supported by MicroManager, in that case it is necessary to connect one of the Arduino outputs to the camera trigger (you need a camera that supports external trigger!). 

Gabriel G. Martins,
10 Jul 2014, 15:48