System | Tasks | Process | |
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Focus Mechanism It will responsible for focusing the lenses on the sample and will be controlled from a web interface. | lenses holder and rack and pinion | Learn more about microscopy from MicroscopyU | |
Design and print the mechanism |
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Design and fabricate a test mount of the test pattern to discover to test the focus mechanism and discover the height needed for the glass plate. | |||
Stepper motor and driver: Actuate the focus mechanism | Test current stepper board and modify if needed |
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Define stepping needed (rack and pinion and stepping code) | |||
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Test with FTDI and Wi-Fi | |||
Finalize stepper board and mechanism | |||
Web interface or manual control and feedback | Modify the web interface and test it with FTDI. |
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Test RaspberryPi Serial communication | |||
Deploy the web interface to the RaspberryPi and test using its GPIO for RS232 communication. | |||
X-Y Mechanism Will shift the camera into a snake-like grid for sequential images capturing. | Shafts holders and stepper mounts |
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Carriage Will hold the lenses and focus mechanism from the top and the Raspberry pi from the bottom | |||
Machine Control |
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Port virtual machine to the RaspberryPi and figure out how to use RS-485 from it. If failed use the cable. | |||
Modify the web interface to control the machine |
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Enclosure Allows the building of another system on the top and the directional light source. | Enclosure for the mechanism in the base | Design and Fabricate the enclosure |
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Glass base for the specimen dish/slide with silicon pads to minimize shaking |
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Customizable height control for the light source/height of accessory system | |||
Web interface Will be used by the user to interact with the device from the internet | Web server | Redesign and finalize the user interface |
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Program the backend for the images stitching and data logging |
The idea here is to create an open-source, cheap and fabbable digital microscope using common components that can be found at most Fab Labs.
The work here is based on the paper titled "A portable low-cost long-term live-cell imaging platform for biomedical research and education" . And is a part of a new paper by Mira A. Okasha titled "An Open-source low-cost Digital Microscope for Monitoring Biological Specimens".
The original paper uses a motorized platform to capture sequential images which are then stitched together to create a high-resolution image that can be viewed at anytime.
The last state of the project was that the machine was finished and was made out of laster-cutted plywood chassis, mechanism was actuated by GRBL shield and image capture and control was done by a RaspberryPi.
Then using a script I was able to capture images and crop them.
And in ImageJ, stitched the cropped images to create a high resolution image.
I tried to fabricate a board "fabGRBL" which include an Atmega and sockets for the drivers but failed to do so as the locally sourced copper sheets weren't FR-1 and traces broke off many times along with the many end-mills.
I chose to install Raspbian Jessie Lite, the Lite version is the same as the normal version except it isn't loaded with a lot of packages including the default GUI. This is useful to make use of the limited resources of the pi in other operations.
First, Choosing a microSD card. Not all microSD cards; this page on eLinux wiki lists compatible and incompatible cards tested by the RaspberryPi community. I chose to buy the SanDisk SDSDQM-016G-B35 MICROSDHC 16GB as it was available in the local RadioShack and somehow guaranteed as there are a lot of counterfeit SD cards and its family is marked as working in eLinux. Also, 16GB should be enough for data logging.
Then I downloaded a Raspbian Jessi Lite the image form the downloads page. I downloaded the"April 2017" release.
Then to install, I proceeded to follow the instructions for Linux W.
After burning the image to the microSD card and booting the Raspberry Pi, I got greeted with the request of login credentials.
I then entered the default credentials:
Username: pi
Password: raspberry
To be able to work with the Raspberry Pi directly, I wanted to connect to it through the Laptop's Ethernet. I started by connecting the Raspberry Pi's Ethernet port to the Laptop's and from Ubuntu's network manager, I edited the Ethernet Connection "Auto Ethernet"and from "IPv4 Settings" I changed the "Method"to "Shared to other computers" and hit OK.
I then followed the instructions in this Stack Overflow post about setting a static IP address for the Pi which I can use to access the Pi from the laptop.
SSH is disabled by default in Raspbian; So, to enable it I entered
$ sudo raspi-config
then 5. Interfacing Options then SSH then YesI then was able to access the SSH by entering
$ ssh pi@10.42.0.63
where 10.42.0.63 is the new static IP I assigned.In order to access the pi faster I added the following line to the /etc/hosts file.
10.42.0.63 faboscope
which enabled me to access the pi by calling this hostname.$ ssh pi@faboscope
In order to be able to test out the optics and maybe stream the camera feed to the web interface. I went on to install RPi-Cam-Web-Interface by following the instruction in their page.
I was prompted if I want it to start, I chose yes and then on my laptop I browsed to http://faboscope/html
Using the MTM inventory , I designed the XY mechanism in inventor and exported the STL files to be printed and the G-code of the base be cut on the CNC router.
I then designed the gantry and carriage for the sensor using the same parts and a laser-cut plywood with various mounting point to determine the proper place for the components to be mounted on.
I cloned the pyGestalt repo and used the xy_plotter.py as a starting point.
Then connected the boards to the motors and to each other and then to the PC using a Fabnet adapter that uses 499 Ohm resistor instead of 600 ohm mentioned in the tutorial .
I edited the moves list to make a rectangular movement to test the motion and tested the speed "velocity" of the movement.
The platform will be used to hold a glass piece where the specimen will be placed. To minimize shaking.
In molding and casting week, I molded a mold of the pad and casted it in rubber silicon.
I then created a linear pattern of another three pieces and casted rubber silicon.
Component | Vendor | URL | Image | Item Price | Count | Price | Notes |
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Mechanical Elements | |||||||
AQS Nema 17 stepper motor with in-built lead screw (4 starts-2mm pitch 8mm dia) | AQS Alternative | MTM BOM | $28.39 | 2 | $56.78 | - Exists in the lab's MTM kit - Will drive the X-Y mechanism | |
Gestalt Boards | N/A | MTM BOM | $15.2 | 2 | $30.4 | ||
USB to RS485 Cable 5.90' (1.80m) Unshielded | Digi-Key | Link | $30 | 1 | $30 | ||
Light Duty Dry-Running Sleeve Bearing, 1/16" Flange Thickness, Nylon, for 3/8" Diameter, 1/2" OD, 3/8" Length | McMaster-Carr | Link | $0.59 | 8 | $4.72 | ||
Highly Corrosion-Resistant 6063 Aluminum, Anodized Tube, 3/8" OD, 0.070" Wall Thickness, 6 Feet Long | McMaster-Carr | Link | $9.56 | 4 | $38.24 | ||
Optics | |||||||
12.5x Magnification Eyepiece Lens | PZO | Link | $9.01 | 1 | $9.01 | Salvaged from an old microscope | |
10x Objective Lens | PZO | Link | $49 | 1 | $49 | ||
Raspberry Pi 2 Camera Module | Raspberry Pi | Link | $20.64 | 1 | $20.64 | ||
5V Unipolar Stepper Motor | Local Market | Link | $4.95 | 1 | $4.95 | Will control the focus mechanism of the lenses | |
Control | |||||||
Raspberry Pi 2 Model B | Raspberry Pi | Link | $35 | 1 | $35 | - Will control the X-Y and focus mechanisms - Capture and stitch imaged - Operate the web-interface and data logging | |
SanDisk SDSDQM-016G-B35 MICROSDHC 16GB | SandDisk | Link Link | $7 | 1 | $7 | ||
Power | |||||||
24 Volt Power Supply - 1.1 Amp Single Output | Circuit Specialists | Link | $13.40 | 1 | $20.64 | ||
Power Barrel Connector Plug 0.70mm ID (0.028"), 2.35mm OD (0.093") EIAJ-1 Free Hanging (In-Line) | Digi-Key | Link | $1 | 1 | $1 | ||
2.50mm (0.094", 3/32", Sub Mini, Miniature) - Headphone Phone Jack Stereo Connector Solder | Digi-Key | Link | $1.13 | 1 | $1.13 |