Generally on dev boards (Arduino's) it is mostly practiced on the GPIO's to use Pullup, because it reduces the risk of being affected from unwanted noise.
Can the same be said about the Axo ?
I am planning on driving the Axo inputs with an Arduino Due and will use a volt level shifter to adjust, but it means I will need to run the signal from the Due back to front and both rise and fall edge triggers back to front on the Axo.
GPIO Pullup versus Pulldown resistors
It seems the Arduino Due runs at 3.3V, so as far as I understand you don't need any level shifter between Due and Axoloti.
Each of the 54 digital pins on the Due can be used as an input or output, using pinMode(), digitalWrite(), and digitalRead() functions. They operate at 3.3 volts. Each pin can provide (source) a current of 3 mA or 15 mA, depending on the pin, or receive (sink) a current of 6 mA or 9 mA, depending on the pin. They also have an internal pull-up resistor (disconnected by default) of 100 KOhm.
The Arduino Due pins can both sink and source current, so they actively drive either 0V or 3.3V. That means you do not need any pullup or pulldown resistors enabled.
You only need pull-up or pull-down resistors if the pin might otherwise be left floating right? For example if there's a switch or button connected?