Cameras for tracking phenology

[DeirdreLoughnan]

@lizzieinvancouver @sandyie @afong3 @buniwuuu @ngoj1 @soleil-nocturne123 @wangxm-forest

We discussed today at lab meeting buying cameras to eventually be used to automatically photograph and track phenology across the growing season (for example, tracking a single grape or a single leaf).

If anyone has an idea for what kind of cameras we could buy, please add them here. @sandyie had the interesting idea of using a network of door bell cameras.

Ideally the options should be, robust, weather proof and wireless.

[dbuona]

Once upon a time I started setting up a raspberry pi camera for this purpose. I never fully got it off the ground, but they are cheap and there are a ton of resources for using them as wildlife camera traps or remote timelapses. https://pimylifeup.com/raspberry-pi-time-lapse/

[afong3]

I'd second a raspi camera setup (or equivalent) connected to some sort of cheap low power development board. This could be a great use case for a Fuse 3 3D printer if we end up acquiring one, too. Waterproof custom enclosures could include whatever other electronics / batteries needed.

I like this deep sea camera a lab built with a raspi camera and Form 3 parts.

[lizzieinvancouver]

@DeirdreLoughnan @afong3

Based on the git issue (thanks Deirdre!) I am busily trying to find a company that sells raspberry pi cameras and would give a CFI discount ... can you guys send me the contact email or contact email website form for any you can think of and I will reach out?

@dbuona Where did you order from?

[DeirdreLoughnan]

@lizzieinvancouver the first one to come to mind is Mouser Electronics, which is based out of Kitchener Ontario. Their email is: canadasales@mouser.com

[lizzieinvancouver]

@afong3 @DeirdreLoughnan Which raspberry pis do we need (and any accessories)? Mouser discounts by item so I need some item numbers ... Thank you!

[afong3]

@lizzieinvancouver @DeirdreLoughnan We have the Raspberry Pi Zero and Raspberry Pi Cam V2 (which have been used for phenology monitoring) in the lab currently, which Mouser stocks as well. In order to use these in a low power scenario though, we would need to do some electronics design with an external timer to power the Pi on / off.

Other options can be ESP32 based, which have a low power mode natively.

• With autofocus!

Another cool one is with a K210 CPU which I've never heard of but apparently does great with low power AI vision models.

• Dev board

These would probably be a good start to test for our specific use case.

[ngoj1]

From questions about lab camera during Scrum 19 March 2024:

For reference the current DSLR in the lab is Canon EOS 30D and the best magnification the lenses we have can offer is 1:1. CaptuRING researchers used a Tokina 100mm f/2.8 AT-X PRO 1:1 Macro (I think, I had to look super closely at their images) lens for their construction.

The technique for taking photos at multiple depths and then stitching them at the parts of highest definition is called focus stacking and is a very common technique for macro wildlife photographers, and there are also plenty of tutorials online for doing this manually (although given we're in this lab, it makes the most sense to try and automate that somehow?). Focus stacking can be done in Photoshop which we should all have easy access to.

[lizzieinvancouver]

@ngoj1 and @afong3 Thanks! Is there a macro you think we should get for our Canon in case we want to try it? (We also have a macro I think... but I am not sure what we would need.)

[ngoj1]

The Canon MP-E 65mm f/2.8 1-5x offers the greatest level of magnification among the macro lenses (up to 5x life size), here's the link to the product on Best Buy. It's quite expensive at $1469.95 CAD, but it has quite a lot of good reviews across the internet.

Pros:

• You manually set the focus or magnification and then move the camera away or closer to your subject, high customizability
• One of the best macro lenses right now for its magnification power and compatibility with EOS camera bodies with good balance between recency of release and established user reviews
• Potential future uses in this lab include imaging minute phenological stages that are harder to capture with other lenses, like pollen dehiscence or stigma receptivity

Cons:

• Very expensive; almost twice the cost of the Tokina 1:1 macro lens above; not to mention there already is a 1:1 macro lens in the lab
• Due to its manual specification, changing the settings may take a while if our samples vary greatly
• Pointless if 1:1 macro lens is already good enough to capture what we need
• Likewise for future use; if phenology of fine-scale organs or structures is not often studied, a 1:1 macro lens would be good enough for more conspicuous events like flowering.

I can't remember if the 1:1 lens in the lab was already tested on these cores, but if it's not good enough AND we think there is potential for use in other experiments then this lens might be a good purchase. I would have listed other ones like 2x magnification, but apparently they're quite clunky to use.

[afong3]

@ngoj1 @lizzieinvancouver Thanks for the research on this! If we already have a 1:1 macro I think it would be fine to not upgrade. Focus stacking seems to be a decently documented problem (one more) , and we can probably replicate it. We also have another backup plan which can be to implement some sort of autofocus because we'll have control of the lens's distance to the cookie with a motorized Z-axis.

[lizzieinvancouver]

@ngoj1 @afong3 Thanks for your work on this! I agree that sticking with what we have sounds good for now ... especially as I think we will want an autofocus lens. See a related comment about light on Tree Ring issue #11