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|
|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|
|Define stepping needed (rack and pinion and stepping code)|
|Test with FTDI and Wi-Fi|
|Finalize stepper board and mechanism|
or manual control and feedback
|Modify the web interface and test it with FTDI.|
|Test RaspberryPi Serial communication|
|Deploy the web interface to the RaspberryPi and test using its GPIO for RS232 communication.|
Will shift the camera into a snake-like grid for sequential images capturing.
|Shafts holders and stepper mounts|
Will hold the lenses and focus mechanism from the top and the Raspberry pi from the bottom
|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|
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|
|Glass base for the specimen dish/slide with silicon pads to minimize shaking|
|Customizable height control for the light source/height of accessory system|
Will be used by the user to interact with the device from the internet
|Web server||Redesign and finalize the user interface|
|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.
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:
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
then 5. Interfacing Options then SSH then Yes
$ sudo raspi-config
I then was able to access the SSH by entering
where 10.42.0.63 is the new static IP I assigned.
$ ssh firstname.lastname@example.org
In order to access the pi faster I added the following line to the /etc/hosts file.
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.
|AQS Nema 17 stepper motor with in-built lead screw (4 starts-2mm pitch 8mm dia)||AQS|
|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|
|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|
|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|
|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|