On Set in the New Jellyfish Mobile Recording Chamber

Welcome back, fellow Jelly-Lovers! We’ve got lots of exciting jellyfish-based updates below, including revealing videos of our very own clytia hemisphaerica, screenshots from and updates about the tracking software, and information on our new recording chamber. (And, of course, I have photos of the full jellyfish costume from the 4th of July!)

Jelly Videos:

As promised, we will start off with some delightful, ultra-short films starring the infamous clytia hemisphaerica. The first 30-second clip shows a super close-up view of a jellyfish that has caught its prey (brine shrimp). The following 48-second clip displays the varying stages of tentacle length in these tiny jellies (their tentacles elongate and retract at will – you have to see it to believe it!!!).

Above you will find a short video showcasing a few clips of a jellyfish that has caught several brine shrimp! Considering that this full-grown jellyfish is less than 20mm in diameter, the zoomed-in details and quality are easily better than what you would see in the real world with the naked eye!

This second video exhibits the 3 different tentacle states I’ve observed: fully extended/elongated, partially retracted, and fully retracted. It seems that the tentacles become longer and more spread out when the jellyfish is hunting (trying to catch brine shrimp). This behavior would make sense, since elongating/spreading out the tentacles would increase the jelly’s area of coverage and therefore raise its chance of success in finding a fresh meal.

Tracking Software:

Since I received this batch of jellyfish and got them stable in their new homes, I’ve recorded well over 60 trial videos with which to analyze their behaviors. To get a head start on analyzing this data, I decided to try labeling a video by hand. I briefly labelled a 25-minute clip manually to see what the data would look like, and after 2 hours had only labeled 3 minutes-worth of frames. This showed me just how inefficient and impossible this task is without some form of computerized help, like that of the in-development jellyfish tracker.

The screenshot above is packed full of useful information from a video run through the jellyfish tracker. The top left shows a close-up image centered on the tracked jellyfish. The text boxes near the top of the screenshot show properties like frame height/width, frame rates, and total frame counts. The ‘Final Coordinates’ table lists the jellyfish’s position within the video. Finally, the graphs show the X position over time, the Y position over time, and the X vs Y position (the jellyfish’s location in 2D space).

The jellyfish-tracking software can now track jellies somewhat accurately (thanks to Stan’s immense help), if given a clean trial video as input. However, slight imperfections in lighting and other environmental variables throw the tracking algorithm off, so the software is not yet robust enough for all the trial footage collected. More tracking algorithm adjustments and video pre-processing steps need to be coded before the software is fully ready.

New Recording Chamber:

Part of the problem I ran into while doing recordings for different trials was control and reproducibility of environmental variables (like lighting) and protecting the water from external air-borne contaminants. A reusable, enclosed testing chamber seemed to be a good solution for my problems.

The first recording chamber was the inside of a cabinet (pictured below).

While it was better than nothing, the cupboard setup was not consistent: there was nothing to hold the petri dish/phone in the same position each trial. Also, having to duct tape the phone (our recording device) for each recording was quite time-consuming (not to mention a gamble as to whether the phone was turned on, auto-focused, or even recording during the trial since the screen was facing the shelf). On top of these problems, the cupboard was in a small closet-type room that does not allow for too many people inside, and the room was often in use by others. It became apparent that a better recording chamber needed to be manufactured.

The photo above shows the progression from pieces of scattered plywood to the new, mobile recording enclosure. This setup is much more consistent and solves most of the problems I’ve listed with the previous attempts.The bottom of the recording chamber has a circular cut-out that is barely larger than the petri dish used for 2D recordings, so placement of the dish is consistent each time. There is a rectangular opening in the front through which everything gets placed (petri dish, sea water, jellyfish and all) which is covered by a black cloth when not being used in an attempt to limit external contamination. This cloth also blocks out the light in whatever room the recording chamber is in, so lighting can be consistent across trials. The hole in the top of the chamber is where the camera goes, and since the phone is placed face-up over the recording hole, we can start/stop recordings, focus the video, and see what’s going on inside the recording chamber during the entire trial! Also, this contraption is mobile, so I can record wherever I need without worrying that a specific room would be in use.

My DIY Jellyfish Costume:

Finally, I’ve added some photos of my homemade costume from the 4th of July, which you may have already seen in another post on the BYB blog: in my previous update, I previewed the costume and the Fellows Summer Experience post showed it as well!

Beauty is in the eye of the Bee-holder: studies with a hive begin!

Why can’t we Bee friends? Bees (unsurprisingly) don’t do what I want them to

Hi everyone, your favorite amateur beekeeper checking in! Since my last post, I’ve moved up to the exciting step of testing on a full hive! The good news is, I’ve gotten over any lingering fear of bees (see my first post). The not so good news is, I am not a bee whisperer and not surprisingly, they don’t want to do what I want them to do, even though I dressed as a queen bee for the Fourth of July Parade! I guess it has more to do with “pheromones” and “being the right species” than great costumes.

living the queen bee life with Maria

On the more scientific side, I’ve learned a lot about bees and my experimental setup in the past few weeks. I built a rig to suspend my landmark elimination cloth above the tunnel in the field, and switched to a white cloth to allow enough light in. It looks like this:

in the lab

in the field

I also learned that things that work well in the lab don’t always translate to (in this case, the literal) field. But half a bottle of super glue later, the tunnel was up in by the hive. Now I just had to get the bees to forage in it.

the tunnel on day one in the field (featuring stylish beekeeping attire)

However, the bees didn’t seem to want to forage, even with the feeder at the end of the tunnel. I moved the whole tunnel closer to the hive entrance, and they seemed to get the idea. I was able to move the feeder back gradually, and as soon as it gets into testing position I can start my trials! …or so I thought, but the path would not be that simple. No sooner had I left my beautifully constructed (if I do say so myself) landmark elimination setup over the tunnel, than the wind knocked everything over a couple hours later! I was able to repair the damage, but I was back to square one. How could I get my pollinating friends to forage for science??

The answer, it turned out, was right there: pollen. These particular bees were finding plenty of nectar (like the sugar water I was providing), but there was a pollen deficit in the environment. By tempting them with pollen as well as sugar water, I was able to lure them into the tunnel. And now, the real fun begins: data collection! Will these bees learn to forage the way I want? Will I be able to construct a stable tunnel of a different diameter? Will I finally succeed in confusing them instead of vice versa? Stay tuned to find out!

There’s a lot of waiting involved, so what do you do? Play with perspective photography, of course!

A Peagrim’s Progress, or, “Let’s get down to pea-zness”

Hello! There has been some trial and error since my last update. I started my experiment with Monica Gagliano’s protocol (overly simplified!):

1. Grow seedlings, 48 of them:

2. Get them used to 8 hours of light, 16 hours dark (circadian rhythm):
3. Train them under decision covers for 3 days:

4. Test them

She had 48 of them. Unfortunately, each of those PVC pipes are $16 each:

PVC (above) x 48 = $768

Well, that’s not very practical for a classroom experiment.

So I tried my DIY version.

1. Take a plant cell box:

2. Make cardboard covers for each of those 48 cells

Fit the covers over the plant cell box:

Make fan/light circuits for them:

Hook them up:

Here is the schematic:

So in this way, 48 plants are being trained with two circuit boards.

That was in theory.

In reality:

1. Cardboard is way too flimsy to stay on the appropriate columns.
2. The fans, 5V, to work with the LittleBits circuits, were way too weak.

Everything kept sliding around, falling apart, as I was supposed to be training them. I was Chi-Fu trying to keep soldiers in line when I needed to be Captain Shang.

The results?

Pea-tiful 🙁 

They grew as straight as sticks, when I was looking for this result:

Plants that grew towards where I presented the fan last, towards the middle of each of the two rows.

The plants also were tall and spindly, meaning they had tried to get to the top as quickly as possible.

So back to the drawing board. We decided to do everything PROPERLY this time. Stick to the protocol. Exactly.

One problem I’d had was everything slipping all over the place so I bolted things down:

We’ll start with a small n of 4. I have another experiment design coming up, but you’ll have to wait until the last post for this and hopefully more exciting data!