After coming back from our trip to Assam, I have had some time to reflect on experiences in India. It was an absolutely tremendous experience; and in a short period of time (a week); we were able to train and expose of the order of 500 students with tools like Foldscope; but more importantly the curiosity that drives us every day. I made new friends (and renewed old friendships). To give you a perspective; I saw my own brother after several years and he helped us from morning to night running the workshop. It was a very personal experience; and I saw the same emotional reaction in many other participants. @Laks could elaborate more on the same, since he had the presence of mind to actually document the whole trip 🙂

For this post; I want to take an example of something really fun we did in Assam; which is sample local lakes. And these lakes were “full” of Daphnia – amongst other things. We found gobs and gobs of Daphnia in our samples. So many, that I had never seen that many Daphnia in an ml of water before. What was remarkable – I have never seen a “blue pigmentation” in Daphnia; and was thrilled and still thinking about this mystery.

To give you a context on the location, we were on the outskirt of Guwahati.

The “red” star represents the place where we did some sample was collected from.

With the students, I did a quick Foldscope movie of the “beating heart” of Daphnia. This is collected just with my regular Fodlscope; with a 140x lens and an iPhone. So, now you should try to collect a data set like this too. Here I am talking about the value of patience and collecting good data. It’s an important lesson in microscopy – patience pays off.

With this post; I also want to share a quick tutorial on how to use “Fiji” or ImageJ to do some image processing and measure some numbers out of your movies. Say, you are interested in measuring the heart rate of the Daphnia.

“You should know; a beating heart of Daphnia is a great model system to ask questions about how chemicals/drugs influence a beating heart. You can study the hydrodynamics and flow inside the heart to see how pulsations are turned into a pulsatile flow. You could add coffee (quiet literally) to the solution and watch what will happen to the heart beat. Or, for that matter, look at how pollutants like a fertilizer can influence an organisms biology (and ecology eventually). This list can go on and on; it’s about you choosing what you would enjoy to do”

So, on our route to the workshop – we sampled a local lake.

To get live imaging of Daphnia; I made a glass slide with a simple cover slip. I added some double sided tape to create a gap between the glass slide and cover slip and gently pressed a little bit – so as to stop any movement in the Daphnia; although they are still alive. This allows me to do long term imaging of Daphnia (in this case; it’s heart) over long periods of time.

Now; to do some quantification – I used a simple tool in ImageJ (an open source microscopy analysis software – available for free. Download here) . I sometimes use Fiji – which is an equivalent tool but written in Java (download here).

Now, since I know that my phone recorded the video at 30 fps (30 frames per second) – I can import the movie in any of these tools and get every single frame as an image. To get an information on how fast your cellphone records; see the info button on the video.

It’s nice to see that most cellphones will also record the location of the data collected- which is valuable for ecological measurements.

Now; I can draw a simple line across the beating heart – so I can set the profile of the heart muscles for a single frame. Once you press “contrl K” – you get to see the profile of intensity for the given line.

Now, simply using the “reslice” tool (Image->stacks->reslice); I am able to get a beautiful Kymograph (where one axis is space and the other extended axis is time); see image below.

Now, every one of these blips is a heart beat. So you can simply count the number of blips per unit time (where time is given in number of frames). Since I recorded at 30 frames per second; that would mean one image every 1/30 sec = 33.3 msec. I checked this by making sure my number of total frames (1617) multiplied by time per frame (0.033 sec) was equal to total length of video ~ 54 sec. So now, by simply counting number of blips per second I am able to tell what the heart rate for this little Daphnia is; and it turns out to be 22 beats in 3.33 seconds; or 6.6 beats per second or ~390 beats per minute. That;s a remarkable number to think about – much higher as compared to a human heart.. even for a stressed out person being monitored under a microscope.

Now, you can imagine; you can do all kind of experiments and ask questions that you care about; and do the experiments over and over again to get to a point where you are satisfied with the answers you get. It all starts by just dipping your hands in a lake and getting some of the beautiful microcosmos of the lake. When I first sample the lake; I did not know I will be watching a heart beat alive. So next time you watch a lake, imagine the billions of beating hearts that make that lake. That;s something to remember.

cheers
manu

ps: On the more social side; I had a number of conversations with participants. Some of them got captured. I have a lot of material to share; but to give some context – I will share a few long videos of spontaneous conversations with several participants. Here are some reflections and chats with participants:
https://vimeo.com/152221900

To give you a perspective of who attended the workshop; here are a few images of the participants.

I am curious to read posts from participants from the workshop – where they can start taking projects they started forward. To me that is the real test of time.. can’t wait to see what is discovered in the lakes of Assam. Once you make posts; please add comments so I can cite you on this post.

References:

1. NOVEL DAPHNIA TEST FOR DETECTING CHEMICAL POLLUTION

2. Investigating the Effects of Water Pollution on Daphnia magna

3. SHORT-TERM EFFECTS IN THE AVERAGE HEART RATE OF DAPHNIA MAGNA UNDER DIRECT CAFFEINE EXPOSURE

4. For more details on learning quantification tricks with Fiji; see this starting manual from DUKE.