Inspiring, Machine learning, Thesis writing, Uncategorized

ESGI – A Different Type of Conference

Recently, I have attended 141th European Study Group with Industry (ESGI) conference in Dublin. It is a very different type of conference/workshop than what I have been attending so far. First of all everything is free, including food, coffee, snacks accommodation and registration – thanks to funding bodies SFI, UCD, MI-NET, MACSI. Second, it is a great opportunity to meet experts from different fields. Third, there are not so many talks or hurried people and most people are young post graduates and post-docs rather than professors. Everyone is there to learn rather than to advertise their work. More importantly, everything ran smoothly till the end of the conference.

The theme of the conference is that industries across Europe pose 5-6 challenges and 50-100 researchers from EU will solve these challenges in 5 days. It is something like a hackathon. This year, most of the problems from the industry are data science related. Since data science/machine learning is a hot topic, many people opted for these challenges. I opted for a Physics related challenge, that is related to wetting/wicking of rough surfaces. A semiconductor company has been looking for an optimised rough surface that can be wetted as easily as possible.

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Wicking of Surfaces Decorated with Microplillars [1]

Although it seems simple at first glance, it is important to stress that by roughing a surface, wetting can be enhanced many orders of magnitude. For example, if we leave a water drop on a flat surface it takes up to 10 days to spread a diameter of 2cm. While using a optimised rough surface it takes only 10s. Such fast wetting of surfaces has applications in biomedical sensors where for example blood or urine samples can be reached to sensing regions easily.

This problem is interesting as it brought me back into the basics of physics, mainly fluid dynamics. Along with me, there are 13 members who liked this Physics challenge. So we formed as team that consists of 2 professors from Oxford. In the end only 5-6 people remained interested in the project and the rest slowly drifted away. Within our team, we formed sub teams, according to the level of expertise. I worked on my own as I don’t have any particular expertise in fluid dynamics.

Problems were given before we were going to the conference, so I did some back ground reading. In the first day itself, I met the company representative from the semiconductor company who gave this challenge. I expressed my interest to him. I read as many as 20 papers on this topic and came to a conclusion that the most of the things that the company would like to know about wetting of a rough surface were already studied/solved.

So I took the second day completely to read more literature and to make sense of it. On the third day, I narrowed down on 5-6 good papers and analysed them deeply. According to these papers, my conclusions are as following:

1) Critical angle of a drop on a rough surface depends on the roughness and it will be different than the critical angle on a flat surface.

2) The roughness dictates whether a surface can be superhydrophilc or superhydrophobic

3) Most rough surfaces studies are silicon cylindrical pillars on silicon substrate.

4) Dynamics of liquid spreading on a superhydrophilic rough surfaces follows washburn’s law i.e. the penetration length of the liquid front is proportional to the square root of time.

5) One can optimise the geometrical parameters such as height and diameters of the pillars and periodicity between the pillars to achieve faster spreading of a liquid drop on a rough surface.

Overall, we presented our findings. I made some friends. I enjoyed dwelling into other scientific field. I hope these type informal conferences will happen more frequently. I highly recommend my fellow researchers to attend the future ESGI conferences. I am looking forward to attend the next ESGI workshop.

References

Ishino, C., Reyssat, M., Reyssat, E., Okumura, K., & Quéré, D. (2007). Wicking within forests of micropillars. Epl, 79(5), 6–11.

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3d printing, DIY, Inspiring, Robotics

Use of 3D printing in science labs

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First 3D printed prototype without guide rails

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Final 3D-printed tip box holder tray with guide rails and springs to tightly hold the tip boxes in place

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3D printed tip box holder with tip box in place

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Our 3D printed tip holder with Andrew Robot

Andrew Alliance’s Andrew, is an impressive little automatic liquid handling robot. For example, my friend who works in a cancer research lab, uses it extensively in his everyday wet lab experiments. One of the problems associated with these sophisticated robots is that they have a very high cost for their accessories. In Andrew’s case, it uses a spring loaded tray to hold a PCR tube/ tip holder box. This tray doesn’t have to do anything other than holding the box in its place firmly. The company priced it over 300£ which is not well justified. If there is anything that is a bit complicated, is the tray that uses the tension of the spring to hold the box in its position. That’s is all about it. It has no electronic component or anything that could push the price over £10, still these companies price it for over £300. Don’t forget the VAT, import taxes, shipping time and costs involved. 3D printer. These reasons lighted up a solution for us here. We’ve decided to 3D print the holder and fix a spring to it. It took me no more than 2 iterations and now we are flying. While it took a little more time than expected to get the spring to function properly. However, I found what I needed in a knit shop- a small railing that need to hold the spring axially. That’s it and the holder is now in my friend’s lab, doing what it is supposed to do, hold the box in its position. It’s funny how such things are so simple and still these companies price them so high. However, with the advent of DIY 3D printers our jobs are getting simpler, reducing the time and costs involved.

What I’ve learned from this little experience is that, many such accessories, like the Andrew’s tip box holder in this case, once we know how to 3D print and design a few simple designs we could make as many of them as possible. We were able to make 3 holders for less than $30 and in no time. 3D printer made this look a kids play project. This little example, shows a perfect use of 3D printers in scientific labs or for printing DIY stuff for your own daily needs.

Credits: Vamsi, for throwing the problem and providing the feedback. Uday, for his help with fixing the rails and springs

 

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DIY, Electronics, Inspiring, LEDs, Lux, Robotics

DIY Vein viewing Device

The problem with veins:

I afraid of getting injections with syringes as it is a very painful experience. Unfortunately, for some people it is even more painful, if their veins are not clearly visible. In that case, usually nurses try to insert the needles into the body by guessing the vein’s position. Sometimes after three to four trails they have to change the spot and start to probe again for invisible veins. It’s particularly a problem for new born babies. Witnessing that needle punches itself is a painful experience.

Simple Solution:

One of the simplest solution to this problem is illuminating the veins by powerful LEDs. This solution relies on the fact that there is a change in colour of the blood, depending on whether it is carrying the oxygen or not. This change can be easily noticeable when veins are illuminated with red LEDs. By exploiting this fact, a company called veinlite made a device that consists of just LEDs (red and orange) and a battery to power them. It has been proved that this device works but it gets patented thus it costs $200 to $300. There are clones of this device, but they too cost ~$100, so these are not particularly affordable to most hospitals.

Open source version:

However, there is a nice guy called Alex, who made a open source version of veinlite and kindly shared the design files with instructions. Recently, I come across a friend who is suffering from this not so easily visible vein’s problem. Therefore, my friend’s hand was swollen and it’s really painful. So I attempted to build this vein viewer with the help of Uday. We just made a one small change to the original design of Alex, by adding a small potentiometer to adjust the brightness of the LEDs. Below are the few pics showing the build process and initial tests. I hope this will be useful to my friend. We didn’t have the exact switch used by Alex, so we adjusted the hole for the switch in the design accordingly. In the future, we will try the rechargeable battery version, if we find the cause. Please see the videos below to know, how it works.

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Top View of our 3D printed VeinViewer

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Bottom View of our 3D printed Vein Viewer

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Vein Viewer during the soldering phase

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First version printed with a wrong colour of a material.

References:

http://www.instructables.com/id/3d-Printed-Medical-Vein-Finder/

http://www.instructables.com/id/How-to-make-an-affordable-Vein-Finder-for-use-d/

https://3dprint.com/11056/3d-printed-vein-finders/

 

 

 

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DIY, Electronics, Inspiring, LEDs, photography

Webcam DIY Microscope

I have a fascination with DIY microscopes. I have been making microscopes with ball lens and laser pointer lens etc. When these lenses are coupled with the powerful smartphone cameras, they produce highly magnified images of microscopic objects. However, I come across a very interesting webcam microscope through Guadi labs. Basically, when we reverse the lens of the webcam it acts as a microscope. There are many versions of this microscope in the Gaudi labs website, from which I chose the laser cut version for its simplicity. The parts were cut in 2016 when I was in St Andrews, but now only they are assembled as I kept this project in cold due to other interesting projects. The only improvement, I have done is connecting LEDS of different colours to the webcam board in place if its original white LEDS. That way I am planning to excite many fluorescent proteins.

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Webcam Microscope front view

 

Below you can find the microscopic images of cells (~ 30um in length) taken with this webcam microscope. I also took microscopic images taken from smartphone based microscope with laser pointer lens (details will be in another post, see reference 2). Clearly, webcam gives large magnification but small field of view. On the other hand, laser pointer lens gives smaller magnification and large field of view. So these two DIY low cost systems can be handy for biological applications. In fact, I am making one of this microscope for my colleague to quickly screen drug injected cancer cells to know whether the drug has reached inside the cells or not. I will follow up the progress of that project in a future post. I must tell you that these microscopes are far better than the $15 usb microscope attachments that can be bought online.

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Microscopic image of cancer cells taken with webcam microcope under white LED illumination. The slide was stained with a blue dye.

Cells with orange illumination

Microscopic image of cancer cells taken with webcam microcope under orange LED illumination.

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Microscopic image of cancer cells taken with webcam microcope under red LED illumination.

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Microscopic image of cancer cells taken with smartphone based microscope with laser pointer lens under white LED illumination.

 

References:

http://hackteria.org/wiki/index.php/DIY_microscopy

http://www.instructables.com/id/10-Smartphone-to-digital-microscope-conversion/

Acknowledgments:

Dundee Makerspace

Vamsi

Uday

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ARDUINO, DIY, Electronics, Inspiring, LEDs, photography, Raspberry Pi, Robotics

Experiments with a Light Meter

Why I am interested in Light meters?

When I was working in Scotland, I came across photo dynamic therapy (PDT), which uses light sensitive drugs to kill cancer cells. In the entire UK, there are only two PDT centers (afaik), one of which is in Dundee. By visiting the PDT center in Dundee, I realised that after applying the PDT drugs, doctors ask patients to wait in  sun light for two hours. There is no particular reason for exactly two hours of exposure to sun light. Therefore, it is not possible to know how much light dose has been received by the patients. To address this problem, PDT center at Dundee measured sunlight across the UK and Ireland and suggested that  cheap lux meters can be used to measure the required lux dose. I met with one of the PI and discussed about this in detail.

The problem with cheap light meters:

However, most commercially available cheap lux meters can only give instantaneous measure of light. These are originally developed for photographers to know lighting in their photo and building mangers to know lighting in a room. But PDT application  requires the lux values to be logged, aggregated to know whether the required light dose is reached. I think the only way to realise that is through connecting the lux meters to a microcontroller and stream the values to a smartphone. For that I am going to use a cheap lux meter that I can confidently modify after reading this blog post .

What I did:

I ordered the lux meter with a brand name “Ceto”from the same vendor as suggested in the blog post mentioned above. I identified the pins required to tap to get the lux values out. These are the pins on the amplifier. I soldered wires to these pins to read the voltage. So effectively LUX values are converted to voltage values in this lux meter. For example LUX of 290 is converted as 0.288V. I connected these wires to a multimeter to  see these voltage values.

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Guts of the LUX meter

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Zooming inside

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Red wire is signal

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Black wire is ground

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Hot glue to keep the wires in place

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Made a hole to the case to let the soldered wires come out, so that I can feed them into a multimeter

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More hot glue to fix the wires to the case

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Connected the wires to multimeter and we can see the light values appearing on the Multimeter as voltage values.

In the next step, I will connect the lux meter to a Arduino Uno and Bluetooth so that its possible to record the  aggregated lux values overtime time to determine the light dose for PDT treatment. I will write these details in another post.

P.S: It is just one of my hobby project, not related to my research.

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DIY, Electronics, Inspiring, Robotics

DIY Toy Centrifuge

Why I like a centrifuge?

Whenever I see a motor, I think why shouldn’t it be converted as a centrifuge. I like centrifuge as a scientific instrument, especially after seeing Lab on DVD systems to diagnose diseases. Recently, I came across Manu Prakash’s paperfuge, where whirligig/buzzer toy was modified to get high speed centrifuge without using any electricity. Although, I like the idea, it still takes more than 15 minutes to separate blood to any useful analysis such as malaria detection.  May be there are better ways to improve the existing technology to get a better centrifuge, a cost effective, functional, may be little bit funny one. Latest open source models use brushless motors used in drones to make a centrifuge. I would like to try that idea. However, one has to spend at least spend $30 to make such open source centrifuge. I would like to make a low-cost, fun toy type centrifuge, so that we can teach kids about centrifuges without spending so much.

How I made One:

I took a brushless DC motor from a CPU cooling fan and attached a conical shape of plastic that I cut from a water bottle. It looks good, I am getting decent speeds with a power bank or a computer USB. Look at the videos, where I tried to separate milk, which is not possible with this toy centrifuge. I am sure that we can separate some suspension solutions which I will try soon. So far the plus points of my design are that it doesn’t require any soldering, 3D-printing. I am planning to enclose it in a cardboard box for safety reasons, although current version doesn’t spin at high speeds to make any damage.

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Top part of a water bottel

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Attach the cap to a PC fan

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Glue to attach the cap

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Finally, PC centrifuge is here

Future Plans

I am trying to make a centrifuge that can go up to 16,000 rpm, with a system similar to the above. I already designed a 3D printed holder for tubes. I will update about it soon. Until then enjoy the footage of toy centrifuge video.

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Electronics, LEDs

Fancy Christmas Dress with LEDs

Recently, one of my friend told me that he has a fancy dress competition sort of thing in his office. We went  for shopping with a hope of finding a Christmas themed sweater with LEDs, with a hope of winning the prize. I remember seeing them in Primark in the UK, but now I moved to Ireland. In Ireland, Primark is labelled as Penneys, where we didn’t find any such fancy dress. So we bought a sweater, nonetheless with Christmas Trea on it. We decided to decorate that with LEDs. I have some LEDs lying around, which I bought from Dealz (which is Poundland in the UK). Somehow, I sewed the LEDS, but its not a neat job. But I managed to hide the ugly sewing job with another sewing job (see the pics). But the end product is very good.

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LEDs sewed on to Christmas Tree

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Blue and Yellow LEDs

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Only Blue LEDS

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Only Yellow LEDS

 

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Backside with jungle of wires

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Close-up of entangled wires

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Wires covered with a napkin

 

My friend won the fancy dress prize, not because he was the only one to wear a sweater with LEDs, but others have just bought their dresses with LEDs already built into them. Moreover, their LEDs were quite low power ones, which can’t be seen in dark, where as ours is quite powerful. Why not, we are powering with 4AA batteries versus their coin batteries.

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