The paper is now on the bioRxiv preprint server if you are interested in further expeimental details: http://biorxiv.org/content/early/2016/05/15/053470
Before instaling the Twitterscope package, you will need to get an API key, an API secret, a token and a secret token from Twitter. Then you need to update theses values in the script.
cd /usr/local/lib/python2.7/dist-packages/twitterscope-1.0-py2.7.egg/twitterscope
Now change the value of key, sec, token and tokenS, inside the main.py script:
key = [your api key]
sec = [your api secret]
token = [your access token]
token = [your secret access token]
You will also need to change the system account in the main.py script to your Twitter's account:
...
#Filter the returned tweet for a specific user
if((u'@yout_account_name' in tweet):
#Condition for single image acquisition
...
Now you need to get an access token from Flickr and allow your application to delete and upload pictures. Then you need to change these values in the flkr.py script
key = [your api key]
secret = [yout api secret]
First install the required dependencies:
sudo apt-get install python-setuptools python-dev python-pip
Then close this repository and install the Twitterscope package:
git clone https://github.com/pellinglab/minerscope_and_twitterscope.git
cd minerscope_and_twitterscope
python setup_twitterscope.py install
Open a new Python terminal window and import the main script from twitterscope:
from twitterscope import main
The program will promt a browser window to Yahoo!. Enter your credentials. Yahoo! will ask your permission to access the application. Once you recieved the approval message, you can close the bowser and return to the Python terminal. This step is only required once.
To run the program, open a new Python terminal window and import the main script from twitterscope:
from twitterscope import main
You should see the folling on the screen:
@ Name Tweet Location Time
Now the program is running. To acquire image with the microscope, you have to use the keywords inside a tweet refered the the microscope account:
singleImage
diyfocus
diytimelapse
singleImage will return a live image of the sample. Correct usage:
@DIYmicrospe singleImage
diyfocus will allow the user to control the focus of the system. If the current focus level is unknown, the user can use the keyword dofocus, followed by an integer. This will return an cluster of 4 images. Each images correspond to a different positon of the sample stage (requested by the user, 2 closer and 2 further relative to the initial position). Correct usage:
@DIYmicrospe diyfocus dofocus 1
If the user needs to change the sample position along the optical axis, the keywords closer/further followed by an interger will move the sample up or down, by a desired amount. Correct usage:
@DIYmicoscope diyfocus closer 3
or
@DIYmicoscope diyfocus further 2
diytimelapse follwed by duration (in minutes) and frequency (in images per minutes) will initiated a timelapse. All the images from the timelapse are saved onto Flickr, but only the first and the last images are returned via Twitter. Correct usage:
@DIYmicroscope diytimelapse duration 4 frequency 5
The user can also remotely change the name of the sample by using the samplename keyword. Correct usage:
@DIYmicroscope samplename [...]
The user can also remolely ask for help, using the diyhelp. This will return this webpage as a link. Correct usage:
@DIYmicroscope diyhelp
Prior to installation, make sur you have minecraft installed on the Rasperry pi (more info at https://www.raspberrypi.org/learning/getting-started-with-minecraft-pi/software/):
sudo apt-get update
sudo apt-get install minecraft-pi
Clone the repository and install the Minerscope package:
git clone https://github.com/pellinglab/minerscope_and_twitterscope.git
cd minerscope_and_twitterscope
python setup_minerscope.py install
Open minecraft and create a new world. Open a new Python terminal window and wait for the world to be generated. In the terminal, import the "generateWorld" script:
from minerscope import generateWorld
Wait a few seconds, you should see the world been generated. If the player is stucted or the world is not correctly generated, return to the menu, start a new game and run "generateWorld" again.
Now when the world is generated, run the "mine" script from the Python terminal:
from minerscope import mine
Depending on your wire configuration, the left (white) and right (black) blocks will control the focus (up or down). The blue block will capture an image from the camera. The yellow block will display a preview image.