RapID-cell-counter

PyQT graphical interface for high-throughput cell counting for research

New for PyQt5 version

Installing instruction

1. Download Anaconda and RapID source code
   1. Download Ananconda if not done before
   2. Download and unzip the RapID-cell-counter manually: click the green button written code (at the top center of this page) and then click download zip in the dropdown options (or use git clone if experienced)
2. Open terminal
   1. In Windows open Anaconda Navigator desktop app then click on CMD.exe Prompt
   2. In Linux the terminal can be open directly via CRTL+ALT+T
   3. In Mac: open terminal by searching terminal in Spotlight (or Finder). Open the terminal by clicking the terminal app
3. In the terminal copy-paste and press enter for the following code

conda create --name RapID -y shapely pandas pyqt scikit-image matplotlib

Run program

For Windows

1. Open terminal
2. In the terminal, activate conda environment copy-paste and press enter for the following code

conda activate RapID

3. Once we activated the conda environment (which contains all the necessary packages to run the code) we can locate the file (the directory where we downloaded and unzipped the package) and enter the directory to be able to run the program. As an example if we unzipped our file in the Downloads directory we can open this directory using the cd Command. In Linux and Mac, the dashes are / while in windows we use \

cd Downloads\RapID-cell-counter-master

4. Start the software by typing the following code into the terminal and pressing enter

python mainQT5.py

Rerunning the program

To rerun the program once we closed it, we only have to reopen the terminal. Activate the RapID environment. Use the cd to navigate to the directory of the mainQT5.py file and the execute it using python mainQT5.py. Or run the following lines if the RapID source code is in Downloads:

conda activate RapID
cd Downloads\RapID-cell-counter-master
python mainQT5.py

For Linux and Mac

1. Open terminal
2. In the terminal, activate conda environment copy-paste and press enter for the following code

conda activate RapID

3. Once we activated the conda environment (which contains all the necessary packages to run the code) we can locate the file (the directory where we downloaded and unzipped the package) and enter the directory to be able to run the program. As an example if we unzipped our file in the Downloads directory we can open this directory using the cd Command. In Linux and Mac, the dashes are / while in windows we use \

cd Downloads/RapID-cell-counter-master

4. Start the software by typing the following code into the terminal and pressing enter

python mainQT5.py

Rerunning the program

To rerun the program once we closed it, we only have to reopen the terminal. Activate the RapID environment. Use the cd to navigate to the directory of the mainQT5.py file and the execute it using python mainQT5.py. Or run the following lines if the RapID source code is in Downloads:

conda activate RapID
cd Downloads/RapID-cell-counter-master
python mainQT5.py