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OpenAFM

OpenAFM

An open source laser scanning microscope with AFM capabilities, for future use by schools and enthusiasts

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OpenAFM is a project that aims to design and build a low cost open-source atomic force microscope (AFM) for use in schools in China, creating citizen science projects.  We feel that an open-source cheap AFM will open up the nano world and all the wonder and potential it contains, to children and ordinary people. We don't know what they will do with it, but we think it will be interesting to find out!

We also have a blog with loads of info, so check out http://www.openafm.com

So far, the project has been the focus of three summer schools bringing together students for the UK, US, China and Taiwan from backgrounds as diverse as physics, education and art and design.  At present we are still in the hardware devlopement phase, but have already begun conversations with schools attached to Tsinghua Univeristy and have had middle and high school children take part in the event.

We are particularly indebted to the Lego Foundation who have supported all three summer schools, and En-te Hwu and the Stromlingo team who are developing a low cost AFM for researchers, and have shared much of their wisdom and experience to help us get this far. More info on their product can be found here: http://www.stromlinet-nano.com/

This project is licensed under the CERN Open Hardware License for more information please click on the Open Hardware License Tab.

August 28, 2015 at 11:22 PM
Created by joebilkobailey and elliedoney
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An atomic force microscope consists of the following main areas:

  • Optical readout system (in this case the DVD head)
  • A scanning stage
  • Electronic controllers
  • Software

Each of these key areas represents a signifcant challenge from a making perspective:  how do we create an optical readout system that is very sensitive to changes in height but also simple and cheap enough for use in a home-built system?; what design and materials should be used for a scanning stage that needs to move accurately over very small distances and be stable to heating effects?; what electronics are needed to simultaneously feed signals to control the mechanical components whilst reading out the optical signal?; and finally, how do we combine all of this in to an interface that is powerful enough to control an AFM but simple enough to be used by school children and enthusiasts in line with the Open AFM vision?.  

August 28, 2015 at 11:27 PM
Created by joebilkobailey, aryon93, and elliedoney
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By eye, we cannot see anything much smaller than the width of a human hair, which is tens of microns. The nanoscale is thousands of times smaller than this. To see, detect and measure objects at the nanoscale, we need to use microscopes to help us. There are many types of microscope which allow you to look at things you cannot see normally with varying levels of detail, or resolution. The level of resolution depends the physical mechanisms behind the microscope, the sample you are using in addition to the quality of the instrument.

Each different type of microscope is designed to observe different types of objects at different magnifications in different environments. Are you trying to look at a bacteria in liquid, a single atom in vacuum, or something inbetween? Often you may want to use a number of different microscopes to look at the same sample to obtain a full understanding of it, as each microscope will give you different pieces of information.

One type of microscope is an Atomic Force Microscope (AFM). We are particularly interested in this type of microscope as we are trying to build one! Also because they are really useful in understanding a wide range of samples.

How does an AFM work?

An AFM ‘sees’ objects in the same way a blind person might, by feeling the surface using a long flexible stick; lumps and bumps on the surface cause the stick to bend up and down, allowing you to build a picture of it.  An AFM is basically a scaled down record player which can read any surface, not just records, generating pictures instead of music. This idea may sound a bit confusing, but it simply sums up the basic function of an AFM.

In an AFM there are a few key parts; a cantilever, a laser with its optics system, a stage, a box of electronics and some vibration control. By taking these components and putting them together we can make a state-of-the-art microscope.

The reason we say that an AFM is like a record player is that the cantilever tip acts just like the needle in a record player. In a record player there are grooves and the needle moves up and down as it passes over them. The signal that we hear is basically a measure of the height of the record underneath the needle. In an AFM the record disc is replaced by the sample of interest, which can almost be anything with interesting and very small features, and as the cantilever goes over it, it moves up and down like the needle.  The signal that we record is the displacement of the cantilever from its rest position, from which we generate images as opposed to sound.

We generate the electrical signal using the laser and its optics. If we focus a laser on the back of the cantilever then we can monitor the cantilever whilst it moves up and down.  We do this through special types of optics; the cantilever moving causes a change in the reflected light, which is measured as a change in the shape of the reflected laser beam that focusses on the photodetector. We can measure this signal electrically. This signal is quite small so we feed it into the box of electronics. Some of these electronics are used to amplify the signal. This amplified signal can be read out and fed into the computer. This allows us to electrically measure the distance between the laser and the substrate at one point.

With this technology we can really sensitively measure the height of the tiny point on the sample that the cantilever is floating over.  But we are interested in much more than just this point, so we need to be able to move the sample around.  This brings us to the next key component of an AFM, the scanning stage.  By using a carefully designed stage we can use an electrical signal to control the motion of our sample. This means that the sample scans underneath the cantilever. The relative motion of cantilever and sample means that we can collect height data at a number of points. When we get all of this data we can stitch it together on the computer and build up an image. This is our microscope image which can be at pretty high magnifications!

We haven’t mentioned vibration control. This is important in pretty much all high magnification microscopes. Without vibration control you find that the sample moves distances larger than the sample size. This means that in the final image the sample is blurred out and you can’t see it. We need some vibration control to stop the sample moving around.

 When would we want to use an AFM?         

Well AFMs can be used to generate some really high magnification images. In optical microscopes (normal microscopes which just magnify light) you are limited in the feature size which you can see. This is because there is a limit to how much you can focus a light beam. The ultimate limit to how small you can focus a beam of light is around 1um (micrometre). One micrometre is pretty small and so we can see some pretty small things by amplifying light but often the things that we want to see are smaller than this, for example DNA, nanoparticles, viruses, atoms, surface features on bacteria, and all sorts of other things.

One situation where we might consider using an AFM is when we want to see features smaller than 1um. In a really good AFM you can see surface atoms – yeah individual atoms –which are under a nanometre (over 1000 times smaller than 1um!).  Not all AFMs can do this, but they can still get some big resolution improvements over an optical microscope.

When else would you want to use AFM? The answer is quite long – there are lots of things that you can do with AFM so this will not be a comprehensive answer!  An example of one other thing that you might want to use AFM for is nanofabrication (instead of imaging). Nanofabrication is where you make things at the nanoscale. In an AFM you can do this in the same way that you image but instead of looking at a square and imaging it you scan a selected area in a predefined shape. When you image with the cantilever in contact with the surface of whatever it is you are looking at then the cantilever scrapes away a bit of the surface. Wherever you haven’t imaged there will be a residual layer standing proud of the surface. The shape and depth can be determined by setting your scan parameters which provides one simple tool for nanofabrication. This kind of nanofabrication can give features 10s of nm size.

August 28, 2015 at 11:28 PM
Created by joebilkobailey and elliedoney
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This is a helpful explanation - thanks for sharing!
11 months ago

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We believe that a low cost AFM could be a powerful educational tool.  A modular design that can be built in a variety of ways to make measurements of the nanoscale world encourages creativity  and participation in 'hands-on' science and engineering.  

To get a feel for how school students would interact with a home-built AFM, and what they would be excited to explore with it, we carried out a series of workshops (in which Edwin and a team of students built his AFM kit from scratch and took images with it and also worked on a scaled-up, moving lego AFM model) as well as working with high school students on the build.  

We also conducted interviews, which we translated and typed, with Tsinghua high school students at the summer school as well as participating PhD student mentors.  We found out that the group of students who worked with Edwin might understand more about how AFM works than the students that did not attend the workshops. This could be because the students that got to build an AFM from the beginning were introduced to how an AFM really works and the key components that it comprises.  In contrast, the students that worked on the build instead of attending the demonstration in general showed a less comprehensive grounding in their understanding AFM and its applications.  

This finding suggested that AFM is perhaps better understood when students can be involved in assembling a kit from the beginning, step-by-step, but also that actually using the microscope is perhaps the most powerful tool to make students think creatively about its potential applications.  This shows the power that hands-on learning can have, breaking down a complex technique such as AFM in to something that students can not only understand but also begin to think of interesting uses or modifications. 

When asked to explore what they thought an AFM kit could be used for, a variety of applications were volunteered by the high school students.  Interestingly, we found a general trend to be that the boys had more creative ideas, including but not limited to moving/manipulating atoms and building a nano-robot, whilst the girls had more realistic ideas (including a use as a quality control technique in the manufacturing industry).  We reasoned that all ideas, whether outlandish or realistic,  show creativity and engagement.  Moreover, in science often the strange ideas are the best ones!   

It was also interesting to investigate what the UK/US-based mentors had discovered in their time working with high school students.  After chatting with several mentors, it was agreed that the high school students are very smart, interested and confident.  The depth of their knowledge base in areas such as electronics, manufacturing and computing was also very evident (most of them seemed to know complicated things that the mentors confessed to have learnt at university!).

More to come on Education soon!

August 28, 2015 at 11:30 PM
Created by elliedoney, aryon93, and joebilkobailey
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We are developing an online citizen science project using PyBosa and the crowdcrafting server http://crowdcrafting.org/project/lego2nano/

In it partcipants are invited to help analyse images of PM2.5 particles, the pollution particles that effect millions of peopel in China and around the world. 

August 28, 2015 at 11:34 PM
Created by joebilkobailey
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Description of crowdcrafting project design and associated code. 

 

Here they are:

I am attaching the code that I have developed for Version 1. I will send the other one when fixed.

 

If you want to create a new project, do the following:

  1. Create an account on Crowdcrafting.org
  2. Get the API key (in settings, crowdcrafting.org)
  3. Then, go to your terminal
  4. Do: cd “path to the folder with the code”, e.g. cd /home/myusername/codecrowdcrafting
  5. To create the new project: pbs --server http://crowdcrafting.org --api-key MYKEY create_project, where MYKEY is, for example: f21ef1d5-191a-32fa-96be-2c9v31141c73
  6. Then, you need to upload the “tasks”, which in this case it is the image paths together with the calibration factor. They need to be in a CSV file. I will explain later the structure. For now, to upload the tasks, do: pbs --server http://crowdcrafting.org --api-key MYKEY add_tasks --tasks-file filename.csv --tasks-type=csvwhere filename.csv is your CSV file. If you want to delete the tasks, do: pbs --server http://crowdcrafting.org --api-key MYKEY delete_tasks
  7. Finally, update the code by doing: pbs --server http://crowdcrafting.org --api-key MYKEY update_project

The structure of the CSV (comma separated values) file is the following:

In the first line, you have id,picture,calibration which are the tags. ID is just a number, e.g. 1 or 2 or 20000. Picture is the URL to the picture of the particle… e.g. http://www.daniellopez.eu/lego2nano/pictures/20150816_11h18m59sReTrace%20DC%20in.jpeg. Calibration is the calibration factor, representing the number of um per pixel, e.g. 0.028766.

Then, in each subsequent line, you have the actual values. For example, this would be a valid CSV file:

 

id,picture,calibration

1,http://www.daniellopez.eu/lego2nano/pictures/20150816_11h18m59sReTrace%20DC%20in.jpeg,0.028766

2,http://www.daniellopez.eu/lego2nano/pictures/20150816_11h18m59sTrace%20DC%20in.jpeg,0.028766

3,http://www.daniellopez.eu/lego2nano/pictures/20150816_11h23m15sReTrace%20DC%20in.jpeg,0.02632

 

The code is based on https://github.com/PyBossa/app-epicollect). Download it. Then, you will have to modify several files. 

 

First of all, there are two files that you need to change: app.json and project.json. Their structure (in both cases) is the following:

 

{

    "name": "Lego2Nano (v2)",

    "short_name": "lego2nano_v2",

    "description": "Pollution particle measurement using AFMs",

    "question": "Size of the pollution particle"

}

 

This is important… If there is another project on Crowdcrafting.org with the same short_name, you won’t be able to create the project; instead, you will get an error. Therefore, the short_name has to be unique.

 

Then, modify long_description.md and long_description.html to get a different project description, and tutorial.html. In addition to modifying the contents… in tutorial.html you will find references to the short_name of the epicollect project. Make sure to modify it to the correct short_name, e.g. lego2nano_v2.

 

Then, they key file is template.html. This is the one that does “everything”. I have attached the one I created. Again, here you will have to modify the short_name so it corresponds to the one of your project. Specifically, there are two sections that you will need to modify:

 

function loadUserProgress() {

    pybossa.userProgress('lego2nano_v2').done(function(data){

        var pct = Math.round((data.done*100)/data.total);

        $("#progress").css("width", pct.toString() +"%");

        $("#progress").attr("title", pct.toString() + "% completed!");

        $("#progress").tooltip({'placement': 'left'}); 

        $("#total").text(data.total);

        $("#done").text(data.done);

    });

}

 

and… (at the very bottom)…

 

pybossa.run('lego2nano_v2');

 

Please let me know if there is any question…

 

All the pictures I got from Edwin are here: http://www.daniellopez.eu/lego2nano/pictures/

Design Files
August 28, 2015 at 11:44 PM
Created by joebilkobailey
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The electronics in our prject has a number of tasks:

  • Drive the piezo stage by converting the digital output signal of an arduino to an analog voltage and amplify it to 10-20V range. 
  • Drive the voice coil actuators in the DVD head which aloow for the focussing of the laser spot onto the surface
  • Extract, process and amplify the signal from the dvd heads photosensitive diodes and calculate the focus errror signal which gives us the information on the distance to the surface or cantilever.
  • Further iterations may need to include feedback and tapping mode controls

August 28, 2015 at 11:53 PM
Created by joebilkobailey
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Intro:

Here are our schematics for laser diode power supply and voice coil actuator controll 

Particlar deisng concerns are the cleaness of the focus error signal, any noise here will result in noise in the image, also stability in the VCA circuit is essential as noise here correlates to motion in the dvd head lense so more noise in the image!

 

Video fo the voice coils moving: https://www.youtube.com/watch?v=enaQ2StXOYY

Tasks Completed:

  • Identification of laser power, PSD and VCA pins
  • Circuit for stable power supply of laser diode
  • Circuit for manual coarse and fine adjustment of VCA's
  • Circuit for extraction and amplifcation of focus error signal
  • Integration on first PCB

Tasks To Do:

  • Redesign PCB with flex cable pins inverted ;)
  • PID for focus tracking feedback

August 28, 2015 at 11:59 PM
Created by joebilkobailey
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To control the AFM we need a user interface that allows the user to select things like scan size, scan speed and move the stage manually aroudn to find different parts of the sample. This user interface must then send signals to the computer physical interface (in our case an Arduino micro) where the firmware converts the user inputs to electronic signals. 

All our code can be found here:

https://github.com/lego2nano/firmware

August 29, 2015 at 12:10 AM
Created by joebilkobailey
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Intro:

Our code is being manged here:

https://github.com/lego2nano/firmware

You may have been wondering what is firmware; it is the part of the AFM that sits between the software interface and the electronics that control the microscope. This means that we need to take care of two tasks: first, to listen to the interface and translate that into a signal that controls the scanning stage. Secondly, we need to measure the signal from the AFM and send it back to the interface. These tasks are accomplished using an Arduino and a microcontroller that we can program to read & write voltages. To do all these things at the right time and in the right order, we control the behaviour of the Arduino using C++ code, we wrote this over the past two weeks.

There are four distinct classes that handle all the problems that our microcontroller might encounter:
– The RTx class: that handles the reception and transmission of data between the Arduino and the Interface.
– The DAC controller class: that controls the motion of the scanning stage.
– The signal sampler class: that is in charge of measuring the signal the electronics team has prepared for us.
– The scanner class: that controls the three other classes for complete scans.

To control the stage, we need to smoothly control the voltage output over a range of voltages.
The problem is that our Ardunios can only send bits (only ‘high’ or ‘low’ voltages and nothing in between). To overcome this problem we need to use a ‘Digital to Analog Converter’ (DAC) (More info and detail here). Microcontrollers can talk to DACs using the so called ‘Serial Peripheral Interface’, this defines which bits we need to send for the DAC to understand what we want. The DAC we use takes one byte as an input, which means we can define our output voltage to be one of 256 discrete levels. Our DAC controller takes care of all this and makes control of the position of the scanning stage a breeze.

 

The signal sampler can jump into action and acquire data once the DAC controller has moved the stage by a certain amount. The two analog outputs provided by the electronics team is sampled several times (default value is 5). Each pair of values is added together to find the total focus error of the DVD head. Under the right conditions, this corresponds to the distance between sample and DVD head. Lastly, the median of the samples is taken as the true measurement, to reduce sensitivity to noise.

The scanner class coordinates the interplay between the other classes, to acquire an entire image.
This is done by having the DAC increase the output by one step, sampling that point and repeating that process to scan an entire line. Afterwards, the scanner will decrease the voltage again, scanning the same line in reverse direction. After one line-scan we need to send the data to the interface (due to low memory on the Arduino).

To send data, the RTx class starts listening for the ‘ready’ command from the interface. This way, we ensure that the interface is ready to receive more data and we are not scanning faster than they can receive and plot the data. After the data is sent, the scanner will do another line scan and iterate until the entire image is sampled.

To Do:

  • Add functionality for switching between reflectivity and focus error signal modes

Design Files
August 29, 2015 at 12:13 AM
Created by joebilkobailey
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Intro:

We decided to create the user interface with Electron, a framework for creating cross-platform desktop applications. Just like a website, Electron uses a code-base of Javascript, HTML and CSS to create interface windows. This means it could be easily understood and customised by anyone familiar with web development – probably the most ubiquitous form of programming.

 

However, unlike a website, Electron allows our interface to be packaged and distributed as a regular desktop application: downloaded and installed as a single file, opened with the click of an icon and easily able to interact with connected hardware and save data to your computer.

Although there are Javascript libraries for controlling Arduino we have decided that in order to increase the speed of the AFM and make the code more efficient and readable we will write our own simple serial communication protocol for this. This has required working closely with the firmware team to decide who takes responsibility for pre-processing the data and controlling the stage (them). The basics of this protocol have been worked out with only high-level commands and confirmation handshakes sent over the serial connection such as “Initialise”, “Start”, ” Data Received” etc..

We have also been working on the front end of the interface, with people coding the control buttons and surface plotting in Javascript as well as sketching layout designs of the interface windows.

 

Tasks Completed:

  • Succesful send of scan and receive data

Tasks Ongoing:

  • Cancel and restart scan function
  • Adjust image contrast
  • Flip scan axis
  • Change scan size/speed

August 29, 2015 at 12:18 AM
Created by joebilkobailey
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Intro:

The major role of the mechanics team is to design a holder for the optical read-out unit, build the scanning piezo stage and think of an effective way to isolate the system from sources of mechanical and acoustic noise.  This all needs to combined in a design that is low cost, compact, robust, easily assembled and aesthetically interesting!

 

Design Files
August 29, 2015 at 12:30 AM
Created by aryon93 and joebilkobailey
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Intro:

Vibration isolation is key to the systems perfromance. Vibrations from people walking, fans in a buildings air conditioning system, air flow or just voices nearby can cause movement on the nanoscale. As such we must isolate our system from these sources of noise, we do this in two ways, firstly shielding it using a sound nsulating box, and secondly plaing it on an antivibration platform. We have been looking at some exciting negative k vibration damping systems but so far the cheapeast and most effective method is a 'borrowed' paving stone and bike inner tube. this combination of mass and spring can remove over 90% of vibrations.

 

August 29, 2015 at 12:36 AM
Created by joebilkobailey
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Intro:

We have made a new stage and connected it up to a function generator. This meant that we could apply a varying voltage across the piezo buzzers. (Piezoelectric materials physically deform when a voltage is applied across them). By applying a time varying voltage we generate time varying motion in the buzzers and by gluing our stage to the buzzers move our stage.

We are currently running some finite element simulations to understand the precise motion of the stage. We need to quantify the scanning motion and compare that to the vertical motion generated by the set up.

To Do:

  • Test expected motion using FEA
  • Look into thermal stability - perhaps using PCB
  • Try quadrant piezo approach

August 29, 2015 at 12:42 AM
Created by joebilkobailey
Comments (1)
Here is a link about related paper: "Low-voltage and high-performance buzzer-scanner based streamlined atomic force microscope system." http://www.bioportfolio.com/resources/pmarticle/695618/Low-voltage-and-high-performance-buzzer-scanner-based-streamlined-atomic-force-microscope.html
11 months ago

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Intro:

We must take the digital signal, convert it to analoge and then amplify it to control the stage

To Do:

  • Correct aplifier circuit

 

August 29, 2015 at 12:57 AM
Created by joebilkobailey
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Th is project is licensed under the CERN open hardware license. The intention is that anyone is free to copy and modify its findings, we encourage users to share these modifications, ideally here so that a growing community of devleopers improving this project can be built. 

 

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March 4, 2016 at 5:33 AM
Created by joebilkobailey
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This is the current PCB being used to control and read out from the DVD head. There are a number of known bugs:

It is supposed to control the stage as well but the DAC does not have proper resistors, so we are using the old stage amplifier circuit instead

The flex cable pins are inverted so you have to connect it by folding the flex cable so it can go in upside down, alternatively buy specialist flex cable adaptors.

March 4, 2016 at 5:39 AM
Created by joebilkobailey
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The current design for our piezo stage:

Known bugs / missing features:

Cantilever mount must be made in addition.

The holes for the micrometer screws should be separated 120 deg to make it more stable and rotated such that the flex cable is not blocked.

 

Design Files
March 4, 2016 at 5:46 AM
Created by joebilkobailey
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