Welcome to the microCounter repository!
microCounter is a tool designed to assist with analysis of images of microorganisms. This project is deep in its early development stages, be prepared for significant overhauls in the near future. What you see here is merely a prototype of functionality, and things to come.
- Filtering of organisms within an image.
- Population estimates of the selected organism.
- Post processes the image to detect images (FAR TOO SENSITIVE).
- Outputs results in text and image format.
Follow these steps in order to install microCounter on your machine.
Go to https://www.python.org/downloads/ and download the latest version of Python for your machine.
After Python has finished installing - open a terminal (or command prompt on Windows), type "pip --version", and press enter. If you see a response like
If you get an error, Python or pip may not be installed properly and you may have to do some further troubleshooting depending upon your issue.
For Mac and Linux users type:
pip install --upgrade pip
For Windows users type:
python -m pip install --upgrade pip
Type the following command into the command line:
pip install opencv-python
Install Kivy for your machine by following this installation reference: https://kivy.org/docs/installation/installation.html
Type the following command into the command line:
pip install tkinter
The following are instructions on how to properly use micrCounter in its current state.
Assuming microCounter has been downloaded and extracted(or cloned) properly. And the installation requirement have been fulfilled.
Open a command prompt and traverse to the microCounter directory.
Enter into the command line:
python main.py
Load the image
After the image has been loaded, you should see it appear in the interface.
KNOWN ISSUE!! The application will not work properly if you load something besides an image. There isn't a validation step, yet.
The name of the organism - used for output files.
The low and high of the color values which represent a potential organism. Used for filtering, and counting organisms. THIS IS CURRENTLY BEING REDISGNED - DON'T WORRY!
2. Hover over the image, and click on the pixel you wish to use as either the low or high threshold value.
Enter in the size range of the organism (in pixels).
If you have successfully completed steps 1 and 2, then you are ready to Analyze!
After analyzing, results can be found under microCounter/results/. The results of each analysis are recorded in a directory of the DATE_TIME the analysis was recorded at.
The resulting images from the filtering, and post procesing can be found under microCounter/results/DATE_TIME/images. Here are some examples:
Included is a text file which includes the results about the analysis. Here's an example:
-----------------------------------------------------------------------
Source file: C:/Users/alist/Documents/GitHub/microCounter/samples/sample1.tif
Recorded on : 2018-04-20 at 13:05:53
Organism: pseudomonas aeruginosa
=============================== RESULTS ===============================
Area of image: 624100 pixels.
Population range of pseudomonas aeruginosa within 13123 and 4374 organisms.
Size Range: [ 4px , 12px ]
Based on the count of : 52493 pixels resulting from the given thresholds: [ 38 255 8] - [ 59 255 234].
Percentage of area covered by pseudomonas aeruginosa is: 8.410991828232655%
- microCounter is currently being redesigned to exist as a web service.
- Analysis setup will eventually be automatic. Providing more convenience with analyzing large amounts of data.
- Manual analysis setup will be drastically improved.
- New analysis characteristics will be added.
This software is free to use for anybody. Please do not redistribute copies of this software.