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.

microscope

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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ARDUINO, Inspiring, Robotics

Can we 3D print Human beings?

Introduction:

Until and unless, you are hiding under caves, you might have heard about 3D printers. If not, 3D printing is just one step more than 2D printing. In normal 2D printing,  information is printed on a surface (usually a piece of paper).  In 3D printing, we can construct three dimensional objects by continuously printing one layer on top of another layer. Using this advanced technology, we can print plastic toys, concrete houses, custom shaped) chocolates (ah Chocolates :p), cars and even rocket engines. Most of the time, we see hobbyists using the 3D printers to make cool plastic models.

What bio scientists can do with 3D-printers?

They can use 3D printers to print the artificial organs using single (live) cells as building blocks. Recent examples of brain cell, heart embryos, prosthetic skull, and legs are evident of the exponential growth in the 3D printing technology.

That immediately, brings up the question, can we put together the 3D-printeded tissues of heart, brain, skull, skeleton, and nerves to make/3D print a complete animal, even a human being?

Does God permit us to do so?

Most of the religious scriptures tell us that we are all constructed from the basic elements soil, water and air. Bible says 3 elements, Baghadgita says 5 elements and Quran says just 2 elements. So the point is somehow it’s possible to copy the Nature, if not the God.

So can we do it?

Let’s do the math first. A human body consists of 10^14 or 100 Trillion single cells. 50 Million cells die/replaced every second.

Little philosophical pause

That means part of us are die and reborn every day. Can you appreciate the beauty of God’s creation for a moment? How complex giants are we?

Let’s come back to science

Using the current 3D printing technology developed by Prof. Boris Chichkov in Germany, we can print 10^8 single cells per second. That means a complete human body can be printed in 2 hours and 47 minutes. Hold your breath. Prof. Boris Chichkov is claiming that it’s even possible to improve the current technology to print 10^10 single cells per second, we can 3D-print a man/woman in 30 seconds. I don’t know about you, but my heart skipped a beat when I was looking at those numbers for the first time. So many philosophical questions were blowing my mind, and I don’t have answers for any of them.

Why do you care?

Because, printing the individual organs, if not the entire body has some immediate benefits:

  • We can print the organs such as hearts and liver to save many lives.
  • For example, In India 200,000 people need a new kidney every year and 100,000 need a new liver. We can stop people dying due to lack of organ donors.
  • In many cases, like developing countries, organ replacement is a costly affair and it involves many kinds of bad things such as human trafficking. So we can avoid that mess, by simply printing the required organs, like how we buy an injection in a shop.
  • The 3D printed bodies can be used as pedagogic tools to teach biology/anatomy to students. Imagine saving lives of many frogs and rats in scientific labs to learn biology.
  • We can rapidly test the drugs on artificial organs, before going for trails on rats and human beings. It will save serious money and time to develop new drugs.

 

Why do I care?

Because, apart from the above reasons, I am making a syringe pump in recent times. Using that I am going to make a bio printer, not to print organs but to print biostructures such as….I don’t know yet. But why? I am just curious. How? Will tell you soon. Is it my main research? Hell no. It’s just one of my hobby project. So it will take some time to see the pictures and videos of me doing bioprinting.

Take away message:

Yes, it is possible to 3D print human beings, or in general animals (at least in principle). Like any technology, it’s more useful than harmful when used in the right spirit.

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Uncategorized

Key lessons for start-ups

Recently, I have attended a start-up skills meet up organised by Scottish enterprise. One of the presenter is Kelvin, who has more than 20 years of experience as an inventor. The synopsis of his lecture are:

  • Start-ups should always advertise the benefits to the customers rather than the features of the product.
  • It is best to talk to relevant trade associations as they can introduce inventors to potential customers. This is a completely new perspective for me.
  • It is good to call the relevant people directly on telephone. People are willing to help most of the time.
  • We should do as many chicken gun tests (aka failure case studies) on the product before going big.
  • Asking right questions to customers for feedback, which gives invaluable insights for the product.
  • Knowing your business model is very important. One should know whether it is good to sell/rent/license their product.

In the next session, we leaned that there are more than one way of doing marketing. One of the best ways is third party referrals. So getting introduced by some known person would bring us many customers in less time. And it is especially true for start-ups which usually don’t have enough resources for marketing. Knowing the fears of potential customers is also important. It is winning over their fears that makes customers to buy our products. Mr. Kelvin emphasised that sending the demo product to potential customers and taking their testimonials would be one of the best strategy.

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ARDUINO, Raspberry Pi, Robotics

My experiments with stepper motor

Its a different game

At the starting of the project I was thinking that it will be fairly straight forward to hook a NEMA 17 stepper motor to Arduino/Raspberry Pi. After all, I have an experience of connecting a 24byj48 stepper motor to both Raspberry pi and an Arduino, without any fuss. The beauty of this 24byj48 stepper motor is that it comes with its own driver board, all including just for $3 (thanks to China). That gave me confidence, that even if I burn it, I don’t mind.

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But..

now I have a NEMA 17 motor, which is mostly used in 3D printers and CNC machines. It costs around $40 (when we buy from a well known vendor, not from ebay). Now the problem is choosing a correct driver board, as this motor does not come with its own driver. Moreover, Arduino/Raspberry Pi cannot directly supply the enough juice to run these motors.

Choosing a correct driver board

After stumbling upon few options, I found that Poulou’s A4988 driver is most appropriate (thanks to Google). I know people running NEMA 17 with L293D chips (I used them a lot in  my robotic projects to run DC motors). But I am really worried about the shiny (and costly too) new motor, and I definitely don’t wanna burn my NEMA 17.  So, I finally ordered A4988 driver board.

And I fried it..

I followed an excellent connections map (and also the Arduino code given there) from this post on Arduino forums. Almost in every hacker blog/forum, this diagram is posted. I powered my board with 12V wall adaptor. I was thinking that, I was giving enough power to motors. But motor did not rotate at all. I checked my connections, rechecked…and rechecked.

a4988 diagram

 

First problem:

My 12V wall-adaptor does not output enough current output. I don’t know, how I failed to check this minor detail. Anyhow, I have replaced the power source with a 8 AA battery pack. And it rotated. I rejoiced and wanted permanent connections, instead of messing up everything on  a bread board with lose connections.

Second problem:

When I soldered everything on a prototype board, for some odd reason, which I have no clue even now, motor did not rotate at all. I was frustrated. First sign of failure. Went back to breadboard, abandoning the prototype board. I reconnected the motor pins and exchanged connections, quite a number of times.  I hate my hacker mind for tempting do this.

Because..

There is a small warning that says, we should not plug or unplug a stepper motor, when the driver board is powered. I learnt this after reading few forum posts, carefully. What happens, if you ignore the warning. Simply your driver board will be fried. And it happened to me.

How I solved it:

Simply ordered a new board, which arrived in just 2 days, thanks to a ebay UK supplier.  Now with the new motor driver, I have taken at most care and connected every according to the above circuit diagram. My motor is finally running.

But..

still there is a small problem. Motor is vibrating while rotating. It is no where near to smooth running. Googled again patiently. The solution suggested was that interchange the connections going to the Motor. Now, I have checked spec sheet of the motor, colour code of NEMA 17 wires and read quite a few forums. Result is that, interchanging the motor pin connections simply wont work. Back to square one. I suspected that Arduino code might be a problem.

Yes it is..

I have changed now to an excellent stepper motor library written by good guys at Adafruit. I installed the AcclStepper library and it worked like a charm. Finally, my stepper motor is now running smoothly. After spending almost 4 late nights, I figured it out. I am ashamed to waste so much time on such a simple task. But that is how a newbie scientist learns.

Lessons learned:

  1. Never, plug and unplug a motor connections, when the driver board is powered.
  2. Don’t blindly use a high voltage power source, without looking at its current supply capacity.
  3. Better use 8 AA battery pack, rather than a fancy 9V battery.
  4. If you burned a driver board already, that’s alright.  Don’t waste figuring out the connections. Just order a new board. That will save lots of time and save your sanity and few hairs on your head.

  5. Once after figuring out that your motor is working, better use a AcclStepper library, than the raw Arduino code. It would make your motor and your life easy and smooth.

Codes:

Simple Arduino code to test the running of the stepper motor

//simple A4988 connection
//jumper reset and sleep together
//connect  VDD to Arduino 3.3v or 5v
//connect  GND to Arduino GND (GND near VDD)
//connect  1A and 1B to stepper coil 1
//connect 2A and 2B to stepper coil 2
//connect VMOT to power source (9v battery + term)
//connect GRD to power source (9v battery - term)


int stp = 13;  //connect pin 13 to step
int dir = 12;  // connect pin 12 to dir
int a = 0;     //  gen counter

void setup() 
{                
  pinMode(stp, OUTPUT);
  pinMode(dir, OUTPUT);       
}


void loop() 
{
  if (a <  200)  //sweep 200 step in dir 1
   {
    a++;
    digitalWrite(stp, HIGH);   
    delay(10);               
    digitalWrite(stp, LOW);  
    delay(10);              
   }
  else 
   {
    digitalWrite(dir, HIGH);
    a++;
    digitalWrite(stp, HIGH);  
    delay(10);               
    digitalWrite(stp, LOW);  
    delay(10);
    
    if (a>400)    //sweep 200 in dir 2
     {
      a = 0;
      digitalWrite(dir, LOW);
     }
    }
}

 

Now to get smooth rotation of the motor, I have used the following code, which makes use of AcclStepper library.


#include <AccelStepper.h>

AccelStepper Stepper1(1,13,12); //use pin 12 and 13 for dir and step, 1 is the "external driver" mode (A4988)
int dir = 1; //used to switch direction

void setup() {
  Stepper1.setMaxSpeed(3000); //set max speed the motor will turn (steps/second)
  Stepper1.setAcceleration(13000); //set acceleration (steps/second^2)
}

void loop() {
  if(Stepper1.distanceToGo()==0){ //check if motor has already finished his last move
    Stepper1.move(1600*dir); //set next movement to 1600 steps (if dir is -1 it will move -1600 -> opposite direction)
    dir = dir*(-1); //negate dir to make the next movement go in opposite direction
    delay(1000); //wait 1 second
  }
  
  Stepper1.run(); //run the stepper. this has to be done over and over again to continously move the stepper
}


Credits

http://forum.arduino.cc/index.php?PHPSESSID=c4am9ddu9ol3f8i14vu6o3aul7&topic=133894.msg1449404#msg1449404

http://electronics.stackexchange.com/questions/95238/stepper-motor-rotating-but-vibrating

http://www.linengineering.com/resources/wiring_connections.aspx

https://cdn-reichelt.de/documents/datenblatt/C300/QSH4218_manual.pdf

http://www.robotdigg.com/news/26/Reprap-Stepper-Motor

http://semiengineering.weebly.com/blog/stepper-driven-by-arduino-a4988

https://github.com/adafruit/AccelStepper

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