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Revision as of 18:58, 13 July 2014 by P.nanda (Talk | contribs)

Summary: Adapter for the Arduino electronics prototyping platform
Author: Nico Stuurman
License: LGPL
Platforms: Linux, Mac, and Windows
Since version: 1.3.18
Automated Serial Port Setup: Yes
Peripheral device discovery: No
Wiki page: Nico Stuurman
Pariksheet Nanda
Roy Wollman

The Arduino is a low cost programmable digital IO board. It has some digital inputs and digital outputs and can communicate with the computer through a serial interface (that is hidden in a USB connection). A very nice and simple programming language makes the Arduino very simple to program. The Micro-Manager interface to the Arduino consists of an Arduino program (the 'firmware') that you need to upload to the Arduino first. The current version of the Micro-Manager has facilities to use the Arduino as a shutter, and as a shutter that only opens when a TTL is set high (for instance, when the camera is exposing). Also, timed sequences of TTL output can be setup. There are also facilities for programmable analogue out, however, those need connection of a DA chip and requires constructions of a 'daughterboard'/'shield'.

Figure: Functional pinout set by firmware version 2
(Image source .svg file)


Arduino Software

Download and install the Arduino Software for your platform. Establish a connection with your Arduino using the instructions that come with the Arduino software (this includes installing a driver for the USB to serial adapter built into the Arduino.


Then download the firmware source code and copy into the Arduino editor. Send to the Arduino, and your Arduino is programmed to work with Micro-Manager.

Hardware Configuration Wizard


Add the Arduino-Hub. You may want to set the "Verbose" property of the port to 0 to avoid extensive logging of the communcation with the device, especially if you are using the input functionality (which queries the Arduino every second).

Pre-Initialization Properties Description
Logic Inverted causes digital inputs and outputs to be considered HIGH when 0 Volts and LOW when +5 Volts.
Serial Setting Value
AnswerTimeout 500
BaudRate 57600
DelayBetweenCharsMs 0
Handshaking Off
Parity None
StopBits 1
Verbose 0

Peripheral Devices Setup

Name Description
Arduino-Switch Digital output pattern set across pins 8 to 13. See usage in #Digital IO
Arduino-Shutter Toggles the digital outputs pattern across pins 8 to 13. Set all pins off when the shutter is closed, and restores the value set in Switch-State when the shutter is opened.
Arduino-Input Reports, both, the digital and analog (0-1023) state of the analog input pins 0 to 5.
Arduino-DAC{1,2} (Not usually used) Reserved for TLV5618 AOTF Peripheral. There does not appear to be any documentation of this peripheral and seems to be a bespoke AOTF control board built for UCSF.
Initialization Properties Description
Pin Reads all 6 input pins when set to All, otherwise reads the individual 0-5 Pin number.
Pull-Up-Resistor Choose whether the Arduino should use its internal 20 kOhm internal pull-up resistor. If not sure, choose On.

Test Communication

Arduino boards Duemilanove and newer feature an LED attached to pin 13. One can verify the Arduino is communicating by changing the state of pin 13 and verifying the LED changes. Setting pin 13 HIGH requires setting the Arduino-Switch-State to 32 (i.e. 2^5) in the Device/Property Browser. If you added the Arduino-Shutter peripheral to the Arduino-Hub toggle the Arduino-Shutter in the main MM window, or if you don't have it change the Arduino-Switch-State back to 0 to see the LED go off.

Usage Notes

Digital IO

All possible combinations of digital outputs that can be set across pins 8 to 13 can be set by a single number from from 0 to 63, with 0 turning off all pins and 63 turning all pins on.

To choose the set of pins to be on for your Arduino-Switch-State pattern, simply add all the decimal values for the pin from the table below; so for pins 8 and 10 to be on, needs a decimal value of 1 + 4 = 5 to be set in Arduino-Switch-State.

Pin Bit Decimal Value when On
8 0 1
9 1 2
10 2 4
11 3 8
12 4 16
13 5 32

The reason one has to do this is MM encodes the pins as bits in binary. Pin 13 corresponds to the most significant bit 5, whose decimal value is 2^5 = 32. Similarly pin 10 will be bit 2 which is 2^2=4.

Device Properties

Properties Description
Switch-Blank On Allows Low or High.
Switch-Blanking Mode Allows On or Off.
Switch-Label Set the digital output pattern across pins 8 to 13. Allows values 0-63. See usage in #Digital IO
Switch-Sequence Off operates the Arduino in normal "switching" mode.
On enables triggered "sequencing" mode. One defines and upload multiple pattern states to the Arduino using a Beanshell script. Then the digital input signal to pin 2 switches between the sets of patterns. Typically, one would connect the camera exposure signal to pin 2.
Switch-State Set the digital output pattern across pins 8 to 13. Allows values 0-63. See usage in #Digital IO
Input-AnalogInput{0:5} 10-bit value of ADC input.
Input-DigitalInput Value depends on how the Pin initialization property was set. Shows binary state of the input pin, if a single in was selected. Shows the 5-bit value of all input pins if "All" was selected.
DAC{1,2}-HubID (Not usually used) Reserved for TLV5618 AOTF Peripheral.
DAC(1,2}-Volts (Not usually used) Reserved for TLV5618 AOTF Peripheral.

Project Tutorials

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