Weekly Progress
Week 1
In the first week we started by studying thoroughly the Engineering Design files provided by the course instructor and figured out the specific goals of the design. The main goal of this project is to control the trajectory of a magnet in an agarose gel block via a stepper motor and image processing.
After being presented with the design in the class, each member of the group started researching as much as they could, so in the next meeting in the lab, we would brainstorm and decide for a more general plan for the whole design.
In the lab, we got familiar with the electronic components, such as the Arduino and the Arduino IDE. Later on, we made sure to check out the differences between programming languages that we may be going to use for the image processing.
Week 2
For week two, we divided out jobs for each group member to be responsible for over the course of the next 10 weeks. We organized our responsibilities with a Gantt chart:
Magnetic Device Timeline:
Week 2
For week two, we divided out jobs for each group member to be responsible for over the course of the next 10 weeks. We organized our responsibilities with a Gantt chart:
Magnetic Device Timeline:
Week
| ||||||||||
Task
|
1
|
2
|
3
|
4
|
5
|
6
|
7
|
8
|
9
|
10
|
Research and Planning- all
|
x
|
x
|
x
| |||||||
Hydrogel- Chris
|
x
| |||||||||
Build Set-Up- Rei and Haroon
|
x
|
x
|
x
| |||||||
Magnetic Forces- Rei
|
x
|
x
|
x
| |||||||
Motor Control- Chris
|
x
|
x
|
x
| |||||||
Computer Vision- Haroon
|
x
|
x
|
x
|
x
|
x
| |||||
Testing and Revision- all
|
x
|
x
|
x
| |||||||
Final Report Preparation- all
|
x
|
x
| ||||||||
.
During lab, our group worked on our frame design and research for our proposal.
Friday evening we met in the Innovation Studio and finished our proposal, as well as the first iterations of our frame design. We decided on a track with an adjustable platform holding the external magnet and a platform with out motor. This way, we can calculate the magnetic force pulling on the magnetic sphere and can adjust accordingly.
Week 3
Haroon and Rei finished up designing the physical model of the apparatus using Autodesk Inventor. The physical build consists of a frame holding the Logitech HD Webcam C525, a platform holding a petri dish of hydrogel, a rail system for adjusting the relative position between the magnet and petri dish, a 5V stepper motor, a ULN2003 driver board, a cylindrical and spherical magnet, and an Arduino UNO. It operates by placing the motor and external magnet on adjustable tracks oriented perpendicularly to each other.
All the parts have been sent for 3D printing in the Innovation Studio.
See below the first finished part of the design:
Week 4
Week 4 was a productive week for our group. The cylindrical magnet fit perfectly in the stand and a basic batch of hydrogel was created in the Wet Lab.
The PhD student responsible for creating this lab demonstrated her procedure for agarose gel for the class (a full procedure based on her's will be posted to the Tutorials page).
Chris also wrote a base code on Arduino IDE to run the stepper motor, and in the lab it was debugged by fixing the wiring of the motor and the Arduino and made it possible to set the speed of the motor.
Week 5
As the 3D parts have not been printed yet, the team worked fairly independently this week, Rei experimented using magnets with the rudimentary batch of agarose gel, Haroon fine-tuned the image processing in MATLAB and was able to detect circles of different sizes and Chris continued work on communicating between other coding languages and Arduino's IDE.
Week 6
This week was eventful, as a major change in the project was made. After Haroon wrote the code in MATLAB to track the magnet, it was found that the program was really slow and would not be feasible to use it, because the magnet would move that fast that it would be uncontrollable.
So the group has decided to try switch to Python, because there are libraries specific to image processing and it is a faster language overall. Using Python OpenCV to process the location of the magnet in a petri dish is significantly faster than MATLAB, so the group gave up the idea of using Python.
The Motor holder and the petri dish holder are 3D printed, but the slide is yet to be printed due to a miscommunication in 3D lab.
Week 7
Chris was able to create a good, clear and consistent batch of 0.6% agarose gel, and Rei tried to experiment with the distance of the magnets, and it was concluded that 0.6% agarose gel is a bit thicker than what we need, because the magnet moves extremely slowly.
The adjustable tracks for the external magnet is finally printed, and Rei and Haroon created a wooden frame to hold the camera above the petri dish.
Because the petri dish holder was smaller than expected, so we have to use a smaller petri dish luckily, but to fix it, we hot glued its lid in the petri dish holder.
Week 8
Rei programmed a magnetic field calculator using Python and a model in Mathematica, which will help to easier set up the magnets.
Chris and Rei figured out the problem that was going for three weeks with the motor. The group is now finally able to control the stepper motor via Python using the library PySerial. This solved a lot of issues and Haroon immediately implemented the code in the circle detection program.
In the weekend Rei tried to debug the code, by experimenting with different speeds.
The code now runs smoothly and all that is left is the magnet positioning.
Friday evening we met in the Innovation Studio and finished our proposal, as well as the first iterations of our frame design. We decided on a track with an adjustable platform holding the external magnet and a platform with out motor. This way, we can calculate the magnetic force pulling on the magnetic sphere and can adjust accordingly.
Week 3
Haroon and Rei finished up designing the physical model of the apparatus using Autodesk Inventor. The physical build consists of a frame holding the Logitech HD Webcam C525, a platform holding a petri dish of hydrogel, a rail system for adjusting the relative position between the magnet and petri dish, a 5V stepper motor, a ULN2003 driver board, a cylindrical and spherical magnet, and an Arduino UNO. It operates by placing the motor and external magnet on adjustable tracks oriented perpendicularly to each other.
All the parts have been sent for 3D printing in the Innovation Studio.
See below the first finished part of the design:
 |
3D printed stand for external magnet
|
Week 4 was a productive week for our group. The cylindrical magnet fit perfectly in the stand and a basic batch of hydrogel was created in the Wet Lab.
 |
| Agarose and 1X TAE solution heating to 100 degrees Celsius |
The PhD student responsible for creating this lab demonstrated her procedure for agarose gel for the class (a full procedure based on her's will be posted to the Tutorials page).
Chris also wrote a base code on Arduino IDE to run the stepper motor, and in the lab it was debugged by fixing the wiring of the motor and the Arduino and made it possible to set the speed of the motor.
Week 5
As the 3D parts have not been printed yet, the team worked fairly independently this week, Rei experimented using magnets with the rudimentary batch of agarose gel, Haroon fine-tuned the image processing in MATLAB and was able to detect circles of different sizes and Chris continued work on communicating between other coding languages and Arduino's IDE.
Week 6
This week was eventful, as a major change in the project was made. After Haroon wrote the code in MATLAB to track the magnet, it was found that the program was really slow and would not be feasible to use it, because the magnet would move that fast that it would be uncontrollable.
So the group has decided to try switch to Python, because there are libraries specific to image processing and it is a faster language overall. Using Python OpenCV to process the location of the magnet in a petri dish is significantly faster than MATLAB, so the group gave up the idea of using Python.
The Motor holder and the petri dish holder are 3D printed, but the slide is yet to be printed due to a miscommunication in 3D lab.
Week 7
Chris was able to create a good, clear and consistent batch of 0.6% agarose gel, and Rei tried to experiment with the distance of the magnets, and it was concluded that 0.6% agarose gel is a bit thicker than what we need, because the magnet moves extremely slowly.
The adjustable tracks for the external magnet is finally printed, and Rei and Haroon created a wooden frame to hold the camera above the petri dish.
Because the petri dish holder was smaller than expected, so we have to use a smaller petri dish luckily, but to fix it, we hot glued its lid in the petri dish holder.
Week 8
Rei programmed a magnetic field calculator using Python and a model in Mathematica, which will help to easier set up the magnets.
Chris and Rei figured out the problem that was going for three weeks with the motor. The group is now finally able to control the stepper motor via Python using the library PySerial. This solved a lot of issues and Haroon immediately implemented the code in the circle detection program.
In the weekend Rei tried to debug the code, by experimenting with different speeds.
The code now runs smoothly and all that is left is the magnet positioning.
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