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After skratching my head for a couple of months already with AVR Studio and an AVRISP STK500 and the like, I am sick and tired of all this and I would like to install the Arduino bootloader on my Geiger Counter which I bought waay back (and never properly used) from Sparkfun. Than, I will try to upload a sketch on it.

I tried using the arduino IDE. No luck! I see it does boast an ATMEGA328 so it should!

Should I do something in particular?

I am really desperate right now!

Any help is truly appreciated!
Well, which bootloader are you trying to burn to the geiger counter?

There are many different versions of the bootloader - you need to choose the one that matches the processor type (i.e. mega328/mega168/etc) and processor speed (1/8/16 MHz) that your board is running at. Although some of the boards options are given as "3.3V" I think this is essentially refering to processor speed - technically running at 16MHz on a 3.3V board is out of spec per the mega168/328 datasheet.

The schematic for the counter ( ... er-v19.pdf) shows it is a mega328 with NO external crystal (i.e. running on the internal clock source). I THINK (I don't have a copy of the arduino IDE in front of me), there might be an old version of the lilypad bootloader that uses this configuration? (The latest lilypads use a '328 @ 8MHz internal).

If none of the built in configurations match your set up, you could either "hack" a crystal (or resonator) onto the processor, or modify an existing bootloader and re-compile. I'm sure there is one around somewhere though - I'm sure I've used this configuration on one of my home made clones.
Hey! Thank you so much, trialex!

I think I just managed to get the firmware updated with AVR STudio. So I have to try a few things in this configuration before I delve into what you had written. As I finally got this to work (I think) I don't want to spoil it by doing something stupid before I try a few things.

The part with hacking a crystal onto the board sound scary though!

Once again.. I really appreciate your help!!!