Hi,

Since you already have a workable system, it seems to me a simple next step can be to have the RPi trigger the shutter via an MC-DC2 cable (this hack can help).  This way the RPi commands the camera instead of the camera informing the RPi, and you can reuse most of the code you already have.  Not to knock the PX4 which I have no experience with, but this incremental approach might make more sense in your situation than a radical change.

>>>Ideally I'd be able to log angle/acceleration data (IMU), GPS (XYZ)
>>>camera-trigger events (hotshoe of camera) to an SD card. 
The Pixhawk class of autopilots is a good choice. All of that data and much more can be logged, but not all of the hardware versions have the ability to use the hotshoe as an input to trigger logging the position and attitude when the photo is taken. All of them can log when the command to take the photo is sent to the camera but not all of them have the ability to use the hotshoe as an input. The original Pixhawk design is getting pretty old though. We have moved to newer versions that have more memory available for the flight code.
You can use a Cube with a standard carrier board. https://cubepilot.org/#/ecosystem/wiring
and ArduPilot https://ardupilot.org/ to log this data
>>>However, I'm concerned about how difficult it would be to configure the autopilot to 'arm' and start logging at the beginning of a session, since it's not connected to motors or servos. 
That is not difficult at all. Your setup is very common. No need to be connected to any motors or servos in order to arm or start and stop logging.
>>> and power needs are simpler (USB input).
Don't power it off the USB in flight. Use one of the power inputs instead. a) USB connectors are not super reliable and b) we use the presense of USB power to indicate it is "powered on the bench" and there are some differences in functions between "in flight" and "on the bench"
Cheers,
Craig Elder
ArduPilot Community Manager
http://www.ardupilotinitiative.com/whoweare

Nice, where in Zambia are you working? Do you need to transport a lot and regularly?

This recent systematic review might be of interest: 'Unmanned aircraft systems as a new source of disturbance for wildlife: A systematic review'

Abstract

The use of small Unmanned Aircraft Systems (UAS; also known as “drones”) for professional and personal-leisure use is increasing enormously. UAS operate at low altitudes (<500 m) and in any terrain, thus they are susceptible to interact with local fauna, generating a new type of anthropogenic disturbance that has not been systematically evaluated. To address this gap, we performed a review of the existent literature about animals’ responses to UAS flights and conducted a pooled analysis of the data to determine the probability and intensity of the disturbance, and to identify the factors influencing animals’ reactions towards the small aircraft. We found that wildlife reactions depended on both the UAS attributes (flight pattern, engine type and size of aircraft) and the characteristics of animals themselves (type of animal, life-history stage and level of aggregation). Target-oriented flight patterns, larger UAS sizes, and fuel-powered (noisier) engines evoked the strongest reactions in wildlife. Animals during the non-breeding period and in large groups were more likely to show behavioral reactions to UAS, and birds are more prone to react than other taxa. We discuss the implications of these results in the context of wildlife disturbance and suggest guidelines for conservationists, users and manufacturers to minimize the impact of UAS. In addition, we propose that the legal framework needs to be adapted so that appropriate actions can be undertaken when wildlife is negatively affected by these emergent practices.

Mulero-Pázmány M, Jenni-Eiermann S, Strebel N, Sattler T, Negro JJ, Tablado Z (2017) Unmanned aircraft systems as a new source of disturbance for wildlife: A systematic review. PLoS ONE 12(6): e0178448. https://doi.org/10.1371/journal.pone.0178448

Hi all

I would like to know your opinion about this footage:

https://vimeo.com/196847435

I fly drones in this place far away of birds for not disturbing them.

And then National Geographic fly a drone very close to birds to have an excellent footage.

You don't think that they are clearly disturbing them?

Hi!

Interesting subject indeed.

In most cases where UAVs are used in nature "documentaries" it is pretty obvious to a behavioural biologist that the animals were negatively affected.

I know that Sophie Gilbert collected bad examples of wildlife UAV harassment/disturbance at one stage.

This looks like  a great resource, thanks!

Hello Aurelie,

Thank you for sharing this info. I just downloaded the brochure and I am sure I will find it very useful. I have senseFly's eBee Classic, with RGB, multispectral and thermal cameras, and look for cases of using those in nature/biodiversity monitoring/management. I guess the brochure will include some cases. Thanks for sharing.
kind regards, Giorgi (from Georgia)