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Adam @ Hilltop Cottage Using Atmel Studio 6 IDE with Arduino (U...

Adam @ Hilltop Cottage

Using Atmel Studio 6 IDE with Arduino (Uno and Leonardo)
The benefits of the Atmel Studio 6 IDE (if you can get to grips with it) are described in various places so I wont repeat them here. For my
part, I began using it with an AVR Dragon board for programming micrcontrollers directly (i.e. not using the arduino or similar
development boards). I have also started writing some libraries and found the Arduino IDE to be a bit limited. I wanted to be able to use
Atmel Studio to create programs that would also be usable, ideally with no change, on Arduino boards with the Arduino IDE being used.
A further complication is that I have both Uno and Leonardo boards, which have a different processor and so need separate code
There are several guides to achieving this kind of thing (Google atmel studio arduino) but most seemed to be rather involved and not
well suited to having boards with different processors. The best I found, which is not at all involved, was by Elco Jacobs. He approached
the task with the kind of strategy I wanted and his account and example code saved me a lot of trial and error. There were a few points
where I wanted to do things a little differently; this post is about the changes and some experiences along the way. It is partly written so I
remember how it works
There are two main parts to getting things to work: compiling the code and uploading to the arduino. Although I do have an AVR Dragon
and could have used in-system programming (ICSP), I wanted to be be able to use the normal process of using the serial upload over USB
and to leave the bootloader intact.
The end point of the following, which is not as complicated as it looks, is that a new Arduino IDE compatible sketch can be
begun by clicking the New Project icon in the tool bar and selecting one of two templates according to the target board.

1 compiling the code

This is the easier part of the two. The approach taken can be broken down into two: configuring Atmel Studio and creating a C++ harness
within which a verbatim Arduino sketch can be executed. Since there are differences between Uno and Leonardo, I created two versions of
the following steps: one for each board.

1a) configuring Atmel Studio

Start off creating a new Executable C++ project and choose the correct microcontroller type (ATmega328P for Uno and ATmega32U4 for
Open the project properties and select the toolchain set of properties. Under AVR/GNU C++ Compiler you should see several groups
of properties.

Add two entries to locate the source files for the Arduino core and be sure to un-check the relative path option. These are to be found
wherever you installed the Arduino IDE. For me, and for the Uno, they are:
C:\Program Files\Arduino\hardware\arduino\cores\arduino
C:\Program Files\Arduino\hardware\arduino\variants\standard
The second of these would have leonardo instead of standard for the Leonardo board.
If you use any of the Arduno libraries, you must add additional entries to Directories for each one: e.g. C:\Program Files\Arduino

Set the compiler to optimise for size and check the -ffunction-sections option.
In addition, under AVR/GNU Linker, set the optimisation to garbage collect unused sections.

Add two entries (these are applicable for Uno and Leonardo; the first denotes Arduno 1.0 libraries and the second denotes a 16MHz

1b) the sketch harness

Two C++ files are used. One will contain the sketch and one contains a few lines of code to hook in the Arduino core libraries and the
main program from which the usual setup() and loop() components of a sketch are called. I named these sketch.cpp and main.cpp
This arrangement means that if you want to compile the same sketch with different Arduino boards as the target you can use exactly the
same sketch.cpp in two different Atmel Studio projects. The neatest approach would be to point both projects at the same file, rather than
copying it, of course!

If you already have an arduino sketch (.ino or .pde) then the content of it may just be copied and renamed sketch.cpp.
There are, however, two small extras that may be required at the top of the sketch:

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1. if there are any functions other than void setup() and void loop() then it is necessary to add a function prototype. This means that if
there is a function void serialMessage() then you must add void serialMessage(); at the head of sketch.cpp in addition to the
function itself. Google arduino function prototype to find out more.
2. if a library such as EEPROM is used then it may be necessary to change the #include to point to the .cpp file rather than the .h file.
If EEPROM.h does NOT contain a #include <EEPROM.cpp> then you need to point to EEPROM.cpp from the sketch otherwise
the compiler will not find the definition of EEPROM. Wire and SD libraries are even more tedious in that there are 1 or more
additional files to include check the error messages, add the #include and if necessary also add a new directory in the C++
Compiler options.
Keep these extras together and above the body of the sketch with an appropriate comment line if you intend to share the code (or just
want to be neat, keep sane).
As an alternative to adding prototypes manually, it is possible to compile and upload in the Arduino IDE and then to grab the C++ code
that the IDE creates during its compile process. To find where this is, go to File|Preferences and set the Arduino IDE to Show verbose
output during: [x] compilation. This will cause the temporary directory containing the C++, all compiled intermediates and the .hex file
used by the uploader to be revealed. The .cpp should be the same as the sketch but with a few extra lines near the top of the listing.
Replace the template sketch.cpp with this.

This is really just a combination of two of Elco Jacobs files with a few edits. Since things are a little different for Uno and Leonardo, the
main.cpp file differs between the two versions. Remember that the end point is a separate template for each board so two versions are
created rather than having to comment out or uncomment code blocks according to the board in use.
NB: You may have to uncomment or add one or mode .cpp or .h files from the Arduino core libraries. See the "//Unused source
files" but also be aware there may be some not listed in that section.
main.cpp for Uno
1 #define ARDUINO_MAIN
3 // Disable some warnings for the Arduino files
4 #pragma GCC diagnostic push
5 #pragma GCC diagnostic ignored "-Wsign-compare"
6 #pragma GCC diagnostic ignored "-Wattributes"
7 #pragma GCC diagnostic ignored "-Wunused-variable"
8 #pragma GCC diagnostic ignored "-Wuninitialized"
10 #include <Arduino.h>
11 extern "C"{
#include <pins_arduino.h>
13 }
18 // Standard Arduino source files for serial:
19 #include <HardwareSerial.cpp>
21 // Other source files, depends on your program which you need
22 #include <Print.cpp>
23 #include <New.cpp>
24 #include <wiring.c>
25 #include <wiring_digital.c>
26 #include <wiring_analog.c> //analog read/write functions
27 #include <WString.cpp>
28 #include <WMath.cpp>
29 #include <Stream.cpp>
31 // Unused source files:
32 //#include <WInterrupts.c>
33 //#include <wiring_pulse.c>
34 //#include <wiring_shift.c>
35 //#include <IPAddress.cpp>
36 //#include <Tone.cpp>
38 // Restore original warnings configuration
39 #pragma GCC diagnostic pop
44 int main(void)
45 {
for (;;) {
if (serialEventRun) serialEventRun();
return 0;
55 }

main.cpp for Leonardo

1 #define ARDUINO_MAIN
3 // Disable some warnings for the Arduino files
4 #pragma GCC diagnostic push

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#include <Arduino.h>
extern "C"{
#include <pins_arduino.h>

// Arduino Leonardo source files for serial:

#define USB_VID 0x2341
#define USB_PID 0x8036
#include <CDC.cpp>
#include <USBCore.cpp>
#include <HID.cpp>
// Other

source files, depends on your program which you need

<wiring_analog.c> //analog read/write functions

// Unused source files:

//#include <WInterrupts.c>
//#include <wiring_pulse.c>
//#include <wiring_shift.c>
//#include <IPAddress.cpp>
//#include <Tone.cpp>
// Restore original warnings configuration
#pragma GCC diagnostic pop

int main(void)
#if defined(USBCON)
for (;;) {
if (serialEventRun) serialEventRun();
return 0;

Try it!
Given the above, it should be possible to cut and paste the blink sketch into sketch.cpp and compile using F7 or the Build menu.

2 uploading
Uploading can be a bit of a pig. The smooth way the Arduino IDE works is, for me, its main redeeming feature. There are several options
and I began by using the rather nice MegunoLink tool (which may be downloaded for free and a donation made). MegunoLink allows you
to locate the .hex file that is created after compilation and to upload it with ease. It uses avrdude behind the scenes, just as the Arduino
IDE does. MegunoLink also includes a rather nice plotting feature, where you can send formatted data over Serial and plot it in real time.
Nice! The MegunoLink site also gives an alternative recipe for using AtmelStudio alongside MegunoLink.
For better integration of avrdude with Atmel Studio, you have to do a bit of fiddling. A lot more fiddling was required to get a usable
approach for the Leonardo. The end point is upload over the normal USB connection by the click of a mouse or keyboard shortcut inside
Atmel Studio.

Setting up for Uno

Tools > External Tools
Add a new tool, give it a title like Uno Serial Upload and set it up something like this (you may need to change the file paths to match
where you installed the Arduino IDE to and you may need to change COM3):
Command = C:\Program Files\Arduino\hardware\tools\avr\bin\avrdude.exe
Arguments = -C"C:\Program Files\Arduino\hardware\tools\avr\etc\avrdude.conf" -patmega328p -carduino -P\\.\COM3 -b115200
I also checked the Use Output window option, which causes the avrdude messages to appear where compiler messages usually

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A new external tool should be accessible from the Tools menu on saving this data. In use it is essential to first select (click on) the project
in the Project Explorer window. This is so that the $(ItemFilenName) is correct. If you have sketch.cpp selected then Atmel Studio tries to
invoke avrdude to upload sketch.hex, which does not exist.

Setting up for Leonardo

It would have been nice if the same recipe as for the Uno could be followed, with a simple change to the -p and -c flags in the arguments
list. Sadly, the Leonardo needs to be given a kick before it is ready to receive avrdude. This is pretty ugly design IMO. The kick is given
by making a connection at 1200 Baud, waiting a while for the Leonardo to run its bootloader and get ready and only then trying to use
avrdude. The COM port usually changes after the kick and changes back when avrdude finishes. Usually! Yes, usually: sometimes I
found it didnt change back after running avrdude if there was an error condition. You can watch this happening in the Device Manager or
upload a sketch in the Arduino IDE with verbose output enabled (go to Preferences to enable verbose output) to see the alternative COM
The easiest option was to adapt Elco Jacobs Python code, which is what the following code shows. Alternatively, you could just follow
Elcos approach but NB that I had problems due to space characters in the path to my Arduino IDE directory (i.e. Program Files).
1 import sys
2 import subprocess as sub
3 from time import sleep
5 # command line arguments are:
6 # first is the arduino IDE installation dir
7 # second is the arduino board type
8 # third is the .hex file
9 # fourth is the upload port
10 # fifth *** only used if Leonardo; omit otherwise *** serial port used to put leonardo into bootloader mode
12 arduinoPath = sys.argv[1]
13 boardType = sys.argv[2]
14 hexFile = sys.argv[3]
15 port2 = sys.argv[4]
17 if(boardType == 'leonardo'):
import serial
port = sys.argv[len(sys.argv)-1]
21 avrconf = arduinoPath + '/hardware/tools/avr/etc/avrdude.conf'
22 avrdude = arduinoPath + '/hardware/tools/avr/bin/avrdude'
23 avrsize = arduinoPath + '/hardware/tools/avr/bin/avr-size'
25 boardsFile = open(arduinoPath + '/hardware/arduino/boards.txt',
28 boardSettings = {}
30 for line in boardsFile:
# strip board name, period and \n
setting = line.replace(boardType + '.', '', 1).strip()
[key, sign, val] = setting.rpartition('=')
boardSettings[key] = val
# check program size against maximum size
38 p = sub.Popen([avrsize,hexFile], stdout=sub.PIPE, stderr=sub.PIPE)#, shell=True)
39 output, errors = p.communicate()
40 if errors != "":
print 'avr-size error: ' + errors + '\n'
print ('Progam size: ' + output.split()[7] +
' bytes out of max ' + boardSettings['upload.maximum_size'] + '\n')
47 programCommand = [avrdude,
'-F' ,
'-p'+boardSettings['build.mcu'] ,
'-c'+ boardSettings['upload.protocol'] ,
'-b' + boardSettings['upload.speed'] ,
# open and close serial port at 1200 baud. This resets the Arduino Leonardo
57 if(boardType == 'leonardo'):
ser = serial.Serial(port, 1200)
sleep(4) # give the bootloader time to start up
62 p = sub.Popen(programCommand, stdout=sub.PIPE, stderr=sub.PIPE)#, shell=True)
63 output, errors = p.communicate()
64 # avrdude only uses stderr, append it
65 print errors

The idea is to call this bit of python code as an External Tool, similar to the way avrdude was called in the Uno example. You will need to
install Python and pySerial. You may also need to change the PATH to include the directory into which Python was installed. I put the
Serial in the Atmel Studio solutions directory.
This time set up the external tool like this:
Command = python.exe
Arguments = C:\Documents and Settings\Adam\My Documents\Atmel Studio\Serial C:\Program Files\Arduino

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leonardo $(ProjectDir)Debug\$(ItemFileName).hex COM6 COM7

I also checked the Use Output window option, which causes the avrdude or python messages to appear where compiler messages
usually do.
The final argument, COM7 in my case, is the one the Leonardo is attached to when you plug it in. i.e. the COM port you would use in
the Arduino IDE. COM6 is the one that is switched to after the kick. You will find that there is quite a lot of delay when using this
script see the sleep(4) command so do not panic if nothing appears to happen at first.
Obviously, the same python code could also have been used for the Uno case but having already got that one working, I left it alone.

Configuring toolbar and keyboard shortcuts

I dont like stumbling through menus. Use Tools > Customise then select the Commands tab and follow your nose to add a toolbar button
or keyboard shortcut for the External Tool x.

3 a nice-to-have creating project templates

Atmel Studio allows you to create template projects, which you can select when creating a new project. The template includes all of the
compiler options, the processor type and the C++ files. I created a template for each of Uno and Leonardo. And if you just want to grab the
templates (bearing in mind they contain the paths to my Arduino installation): Arduino Uno Arduino Leonardo (copy these into Atmel
Studio\Templates\ProjectTemplates or use File|Import menu). Ive also done a similar job for a library template but with some Visual
Studio placeholders (Atmel Studio is basically Microsoft Visual Studio under a bit of customisation), but only for Uno: Uno Library
Template. The library does not, of course, use the main/sketch convention. Note that, for a reason I cannot fathom, the compiler
optimisation setting (-Os) is not correct when a template is used. It looks OK in the template project file but something goes wrong when
creating a project from the template.
Once you have parts 1 and 2 completed and working (e.g. using the blink example), all you have to do to create a template is File >
Export Template and follow your nose
My templates have no libraries to keep things minimal by default . Hence, when I create a project using a template, any libraries will need
entries in Directories as in step 1a {edit: it might have been better to include them all and to delete lines when not needed}.

4 a recommended Atmel Studio Extension

There is an extension for Atmel Studio that essentially does the same as the Arduino IDE Serial Monitor. It is called Terminal Window
and it can be installed using Tools > Extension Manager. This is not a command window, in spite of what the icon appears to show.
Once installed, the terminal window can be started from the View menu. I chose to dock mine to the bottom of the Atmel Studio window,
which causes it to become a tab alongside the compiler output and errors/warnings tabs.

Licence etc
Elco made his code available under GPL v3 and you should consider the source code given above to be distrubuted under the same terms
since it is a derivative of his work.
* Copyright 2012 Adam Cooper, based heavily on the work of Elco Jacobs.
* See
* This is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
* This software is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* GNU General Public License for more details.
* See: GNU General Public License

This was written by Adam. Posted on Saturday, December 1, 2012, at 9:23 pm.
Filed under Arduino, Microcontrollers. Bookmark the permalink. Follow
comments here with the RSS feed. Post a comment or leave a trackback.



Elco Jacobs wrote:

Great work Adam. I will merge your additions into my code if you are OK with that.
I will also make switching between UNO and Leonardo automatic, by checking if USBCON is defined.
Did you fork it on GitHub?
Saturday, December 1, 2012 at 9:50 pm | Permalink


Adam wrote:
@Elco no I did not fork it. I should have done but I wasnt thinking properly!
Saturday, December 1, 2012 at 10:04 pm | Permalink

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Pete wrote:


Hey this is a pretty good walkthrough, Im struggling with step 1b I think. I am struggling to see how to fit the sketch harness into
the main program. I tried building the main program (using leonardo) but get undefined reference to setup/loop error. Is there
perhaps an example of how you include sketch.cpp or you could possibly give a bit more guidance at these steps. Thank you
Wednesday, December 26, 2012 at 1:20 pm | Permalink

Adam wrote:
OK Ill have a go tho its always hard to diagnose problems remotely and I might have got the wrong end of the stick!
To add sketch.cpp (or any number of supplementary files, for that matter) you can use the menu: Project | Add New Item . Then
choose CPP file and give it a name. You can also get the same result other ways.
You should also be able to just paste the same sketch code into the end of main.cpp instead of having a separate sketch.cpp
(remembering the notes about function prototypes).
Cheers, Adam
Wednesday, December 26, 2012 at 9:00 pm | Permalink
Richard Waterman wrote:


Only had Arduino a few days and hate its IDE. Ive programmed in other languages and miss their editors. The python script is just
used for uploading? You can still program with regular example code of Arduino? (other than the function prototype) I was using a
sikuli library in java and would want to continue to use it here. Should be no problem? And also what about Processing? Can this be
done for that as well? I really cant see how people like these editors lol.
Saturday, February 23, 2013 at 12:58 am | Permalink
Adam wrote:


Yes, the python is just for uploading. There are other approaches you can use to upload too: have a look at Megunolink. Yes, regular
arduino code will work so long as you add the function prototypes and make sure the libraries are referenced. This is dependent on
the compiler and linker rather than the IDE per se. As for the rest, I have no idea
Saturday, February 23, 2013 at 5:44 pm | Permalink

Chris John wrote:

stared should be started
{yes corrected, thanks. Adam}
Sunday, May 26, 2013 at 2:43 pm | Permalink


Antonello wrote:
With the blink sketch Ive received the following errors:
OUTPUT was not declared in this scope
pinMode was not declared in this scope
HIGH was not declared in this scope
digitalWrite was not declared in this scope
delay was not declared in this scope
LOW was not declared in this scope
Then Ive include the Arduino.h inside sketch.cpp and everything worked.
Is that normal ?
Tuesday, June 18, 2013 at 9:22 am | Permalink


Adam wrote:
Yes, you do need to include the Arduino libraries; these functions and constants are not considered standard by the compiler. This
is the case for all of the functions documented on the Arduino Language Reference page
Thursday, June 20, 2013 at 1:59 pm | Permalink


Chris Fisher wrote:

Excellent guide, thank you for posting.
I have the Arduino Micro.
Arduino IDE allows the upload of Blink program example to test functionality. I manipulated the time delays to the LED, while
observing on the scope. So the hardware and software is working correctly thru uploading.
I followed the setup and successfully compiled Blink in Studio 6.1 all files generated no errors. When I run the AVRDude tool in
6.1 I get the following error:
avrdude.exe: Version 5.11, compiled on Sep 2 2011 at 19:38:36

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Copyright (c) 2000-2005 Brian Dean,

Copyright (c) 2007-2009 Joerg Wunsch
System wide configuration file is C:\avrdude.conf
Using Port : \\.\COM8
Using Programmer : arduino
Overriding Baud Rate : 57600
avrdude.exe: stk500_getsync(): not in sync: resp=000
avrdude.exe done. Thank you.
The yellow LED flashes a few times when I run the Upload tool.
I have hi-res photos of the scope the Arduino micro and the Studio 6.1.
Not sure what causes the stk500_getsync(): not in sync: resp=000 Error within AVRDude. I really appreciate any guidence.
Monday, January 20, 2014 at 12:21 am | Permalink

Adam wrote:
Chris Im a bit hazy about the workings of avrdude; I follow standard recipes.
In your case, it looks like the baud rate might be wrong. I think you should be using 115200 baud. See the section Setting up for
Uno on my post.
I think when you upload from the Arduino IDE it picks this up from a boards.txt (somewhere inside C:\Program Files\Arduino)
otherwise getting default values from C:\avrdude.conf if it exists.
Sometimes Windows messes up COM ports. Try a reboot, check port assignments etc if the above does not get you there.
hth, Adam
Thursday, January 23, 2014 at 9:29 pm | Permalink


Chris Fisher wrote:

Thank you for providing some guidance.
Iam still unable to successfully deploy.
Here is the output window, if you notice anything obvious, please let me know.
Deploy script
Executing local-deploy99.bat
Deploying P1BLINKAM2 Build 5
The system cannot find the path specified.
CANNOT Find output file C:\Users\C\Documents\Atmel Studio\6.1\P1BLINKAM2\P1BLINKAM2\scripts\output.txt"
Aborting script
C:\Arduino\hardware\tools\avr\bin\avrdude.exe -CC:\Arduino\hardware\tools\avr\etc\avrdude.conf -v -patmega32u4 -cavr109
-PCOM9 -Uflash:w:C:\Users\C\Documents\Atmel Studio\6.1\P1BLINKAM2\P1BLINKAM2\Debug\P1BLINKAM2.hex:i
avrdude.exe: Version 5.11, compiled on Sep 2 2011 at 19:38:36
Copyright (c) 2000-2005 Brian Dean,
Copyright (c) 2007-2009 Joerg Wunsch
System wide configuration file is C:\Arduino\hardware\tools\avr\etc\avrdude.conf
Using Port : COM9
Using Programmer : avr109
AVR Part : ATmega32U4
Chip Erase delay : 9000 us
BS2 : PA0
RESET disposition : dedicated
RETRY pulse : SCK
serial program mode : yes
parallel program mode : yes
Timeout : 200
StabDelay : 100
CmdexeDelay : 25
SyncLoops : 32
ByteDelay : 0
PollIndex : 3
PollValue : 053
Memory Detail :
Block Poll Page Polled
Memory Type Mode Delay Size Indx Paged Size Size #Pages MinW MaxW ReadBack
- - -
eeprom 65 10 8 0 no 1024 8 0 9000 9000 000 000
flash 65 6 128 0 yes 32768 128 256 4500 4500 000 000
lfuse 0 0 0 0 no 1 0 0 9000 9000 000 000
hfuse 0 0 0 0 no 1 0 0 9000 9000 000 000
efuse 0 0 0 0 no 1 0 0 9000 9000 000 000
lock 0 0 0 0 no 1 0 0 9000 9000 000 000

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calibration 0 0 0 0 no 1 0 0 0 0 000 000

signature 0 0 0 0 no 3 0 0 0 0 000 000
Programmer Type : butterfly
Description : Atmel AppNote AVR109 Boot Loader
Connecting to programmer: .
Found programmer: Id = w(; type =
Software Version = E.avrdude.exe: error: buffered memory access not supported. Maybe it isnt
a butterfly/AVR109 but a AVR910 device?
Deployment Failed
ECHO is off.
Sunday, January 26, 2014 at 2:34 pm | Permalink
Adam wrote:


well, one thing I failed to notice at first was that you are not using an Uno, so my comments on baud rate were wrong.
Maybe try to run avrdude from a command line (DOS Window) and see if that works.
This looks a bit odd: CANNOT Find output file C:\Users\C\Documents\Atmel Studio\6.1\P1BLINKAM2\P1BLINKAM2
\scripts\output.txt Aborting script
It might be a symptom of anti-virus software getting in the way. Ive certainly had problems with compilation due to my AV. Try
disabling it and see if things improve.
Saturday, February 1, 2014 at 5:49 pm | Permalink

David Perrin wrote:

Hi, Do you add the sketch.cpp to your project ? It tells me that OUTPUT is not declared in this scope.
Can you show me an example of your File explorer ? (picture)
Thanks a lot !
Monday, August 25, 2014 at 3:52 pm | Permalink

4 Trackbacks/Pingbacks
1. Adam @ Hilltop Cottage Simulating Arduino Code using Atmel Studio 6 on Saturday, May 11, 2013 at 2:20 pm
[...] This starts off as just a case of compiling the code in Atmel Studio so you can set break-points or step line-by-line through the
code to see what happens. See an earlier post of mine for how to get an Arduno sketch to become an Atmel Studio 6 project. [...]
2. Adam @ Hilltop Cottage Debugging Arduino using debugWire (+ Atmel Studio and an AVR Dragon) on Saturday, May 11, 2013
at 4:14 pm
[...] is basically just a case of compiling the code for the Arduino in Atmel Studio as Ive previously described. It is NOT necessary
to upload the compiled code using avrdude because Atmel Studio will do this [...]
3. How to: Step by step guide to setting up Atmel Studio (AVR Studio 6) for Arduino | aSensar on Sunday, June 23, 2013 at 3:23 pm
[...] Using Atmel Studio 6 IDE with Arduino (Uno and Leonardo) [...]
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