Arduino - Getting Off The Dev Board

The Arduino Uno is a readily available development board for the Amtel ATmega328 microcontroller, allowing the user to easily experiment and iterate with their design. For use in an actual product, or to make a one off gadget even smaller, it is advantageous to use the microcontroller chip independent of the Arduino board. These notes look at operating the ATmega328 by itself on a breadboard, and how to program the chip in situ using an Arduino.

Advantages of Bare Microcontroller


Simplified ATmega328 pinout showing Arduino pin names

Minimal ATmega328 Setup

Minimum setup of ATmega328 with no crystal and single LED for output.

Correctly programmed, the atmega is able to run without any external components, using one of two internal clock oscillators.

Power is supplied to pins 8, 22 (ground) and 7, 20 (+V)

An example is shown above on a breadboard - the only extra components are two .1uF capacitors bypassing the supplies at the chip, and an LED (with 1k resistor) hung off pin 19 (port pin PB5). IC pin 19 is digital pin 13 in Arduino land, where the onboard LED is connected, making this setup compatible with Arduino sketches such as Blink.

With 16MHz Crystal

When greater timing accuracy or a higher speed is required, a crystal can be used for generating the clock - this is the setup used on the Arduino board.

An unprogrammed ATmega328 is supposed to come setup to use the internal oscillator; the examples I had to hand were seemingly preprogrammed to use the crystal so it was required for initial programming.

Same breadboard circuit shown with added clock components - 16MHz crystal and two capacitors.

Programming Connections

Programming an ATmega328 in serial mode from an ArduinoISP requires the following connections:

Arduino pin 10 → ATmega328 pin 1 (RESET)
Arduino pin 11 → ATmega328 pin 17 (MOSI)
Arduino pin 12 → ATmega328 pin 18 (MISO)
Arduino pin 13 → ATmega328 pin 19 (SCK) (Also connected to LED)

It is safe to connect the Arduino board pins directly to target microcontroller as the ArduinoISP sketch handles the communication pins carefully before and after programming to prevent two outputs being connected together. [1]

Programming connections for ArduinoISP

Programming with Arduino IDE

These examples will upload the Blink sketch onto the target.

Programming Arduino Directly

For comparison, this is the usual procedure for programming an Arduino Uno board directly. (If trying this, be sure the Arduino is not connected to the breadboard at this time.)

Note that depending on operating system and setup, the name under Tools > Port may vary. When uploading directly to an Arduino, the setting of Tools > Programmer does not matter.

Making Arduino into ArduinoISP

An Arduino board can be turned into an ISP (In System Programmer) for uploading code to a bare microcontroller using the sketch ArduinoISP.

Pins 10, 11, 12, 13 (and ground - and power if required) can then be connected to the breadboard/in-system microcontroller as given in the hardware section above.

Programming the Bare ATmega328

With an Arduino set up as an ArduinoISP, connect it to the ATmega328 that is on the breadboard or in-system. See hardware section above.

To successfully program the bare microcontroller, we have to set Tools > Board and Tools > Programmer correctly.

The Tools > Board setting is used to determine the processor frequency (for making time based functions such as delay() work correctly), and for setting fuse bits when burning the bootloader.

Tools > Programmer must be set to "Arduino as ISP" to correctly use the Arduino programmed as an ISP.

Basic - with Stock IDE

An ATmega328 setup with a 16MHz crystal can be programmed successfully from the stock Arduino IDE with Tools > Board set to "Arduino Uno".

The crucial step is using 'Upload Using Programmer' on the Sketch menu. This will upload the sketch via the ArduinoISP to the second ATmega. Holding down shift while clicking the upload toolbar button also works. (However see below, a suitably configured board specification will obviate this and allow using Upload as normal)

Choosing Clock with Fuse Bits

Determining fuse bits requires the correct settings in the boards.txt within a platform specification, which is what is chosen with the Tools > Board setting.

The following examples assume the In System MCU platform is installed.

To set the fuse bits, choose a "Board" with appropriate settings and use "Burn Bootloader" - fuse bits can only be written from the IDE when also burning the bootloader.

Note that when reprogramming a used microcontroller, if it has previously been set to require a clock crystal, this will need to be provided whilst setting the fuse bits, otherwise it will have no clock and be unable to communicate with the programmer.

Once the fuse bits have been set as desired using Burn Bootloader, compiling and uploading a sketch proceeds in the usual manner.

Breadboard ATmega328 running Blink sketch using internal oscillator - note crystal is removed.

In System MCU - Custom Platform

I have created a custom platform called In System MCU which provides various useful fuse settings. A zero-size 'bootloader' is provided with each of these board settings, and fuses are set to allow the entire flash memory to be used for the sketch. They are also configured so as to conveniently force the IDE to use "Upload Using Programmer" when the user selects "Upload". [2]

The custom platform is available for manual installation from GitHub, or can now be installed via the Boards Manager:

See notes below on creating a platform specification.


  1. On reset, data direction registers are initialised to 0, making all port pins inputs.

    ArduinoISP - pulls down target's RESET line before setting Arduino's comminication pins as outputs. (Reading ArduinoISP source code: start_pmode() calls reset_target() then calls SPI.beginTransaction() which will set up communication pins as outputs. start_pmode() is called from avrisp() which is called from the loop. avrisp() chooses what to do by calling getch() which calls to recieve communication from the IDE)

    After programming, ArduinoISP sets the communication pins to inputs before bringing the target out of reset. (end_pmode() called from avrisp())

  2. Within boards.txt, leaving out boardname.upload.protocol forces the IDE to use Upload Using Programmer when the user chooses Upload.

  3. Fuses

    Function ATmega328P Default My Fuses Arduino Uno
    High Fuses
    External Reset 1 = Enabled
    Debug Wire 1 = Disabled
    Serial Programming 0 = Enabled
    Watchdog Timer 1 = Not Always On
    EEPROM 1 = Not Preserved During Flash
    Bootsize 00 2048 words 11 = 256 words 11 = 256 words
    Boot Vector 1 0x0000 1 = 0x0000 0 = 0x3f00
    Low Fuses
    Divide Clock By 8 0 = Yes ? 1 = No
    Clock Output on PORTB0 1 = No
    Startup Time 10 = 14CK + 65ms ?? = 14CK + 65ms 11 = 14CK + 65ms
    Clock Select 0010 = 8Mhz Internal ? 1111 = Low Power Crystal 8-16MHz
    Extended Fuses
    Brown Out Detection 111 = Disabled 101 = 2.7V 101 = 2.7V

    CKDIV8 fuse merely detemines the after reset value of CLKPR Clock Prescale Register to be either 0000 (divide by 1) or 0011 (divide by 8). This can be changed from software once the processor is running.

    CLKPR = 0x80;    /* prepare to change prescaler value - required by hardware */
    CLKPR = 0x03;    /* divide clock by 8 (2^3) */

    Useful Fuse Combinations

    High Fuses = 0xDF 1101 1111

    Extended Fuses = 0xFD

    Low fuses:

    Divide by 8 Startup Time (14CK + 65mS) Clock Select Low Fuse Value
    16MHz (8-16MHz+ Crystal) 1 11 1111 0xFF
    2MHz (8-16MHz+ Crystal) 0 11 1111 0x7F
    8MHz Internal 1 10 0010 0xE2
    1MHz Internal 0 10 0010 0x62
    0.128MHz Internal 1 10 0011 0xE3
    External Clock 1 10 0000 0xE0
  4. For low clock speeds (eg. internal 128 kHz) have to slow down SPI for programming in ArduinoISP - change line 53:

    #define SPI_CLOCK 		(128000/6)
  5. Loop doesn't run at low clock speed?

    At low clock speeds, there is not enough time for interrupts to complete, specifically the millisecond interrupt, causing the microcontroller to hang.

  6. Arduino IDE also hides stuff in ~/Library/Arduino15

  7. Platform Specification

    A custom Board can be specified by creating a folder within ~/Documents/Arduino/hardware. Within this folder must be a subfolder 'avr' containing the specification files.

    Required files are boards.txt, platform.txt, and a bootloader .hex file.

    Platform.txt only has to define a name and version. The name is shown as a subheading in the Tools > Boards menu.


    name=In System MCU

    The bootloader must be in a further subfolder 'bootloaders'. It is Intel Hex format; a null file can be created with only an end of file record.



    boards.txt defines various things, including the expected processor speed and fuse bits to use when burning the bootloader. 16 MHz (16 MHz Crystal)

    Package Index Specification

    Installation archive: remove boards.txt, platform.txt, bootloaders/ from avr/ subfolder and place in root of what will become .zip archive. Host installation archive online eg. via github.

    package_????_index.json file to be hosted elsewhere than installation archive.

      "packages": [
          "name": "In System MCU",
          "maintainer": "Jason Bamford",
          "websiteURL": "",
          "email": "",
          "platforms": [
              "name": "In System MCU",
              "architecture": "avr",
              "version": "1.0.0",
              "category": "Contributed",
              "help": {
                "online": ""
              "url": "",
              "archiveFileName": "",
              "checksum": "SHA-256:174415C70E69364FEC88809892618D5B703595DF9BAB97B661345A77A53D7E7B",
              "size": "3284",
              "boards": [
                {"name": "ATmega328P (8-16+ MHz Crystal)"},
                {"name": "ATmega328P (8 MHz Internal)"}
              "toolsDependencies": []
          "tools": []

    To generate checksum and size: download target zip, run `shasum -a 256` and `stat`.