Installation and Quick Start

Page Contents

• Dependencies
• Environment and code packages
• Downloading SCC
• Starting SCC

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Dependencies

SCC requires a Python distribution to be installed.

If you do not have Python, follow the steps on the official Anaconda installation documentation, which will install Anaconda Navigator and Anaconda Prompt.

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Environment and code packages

Code packages which SCC relies on must be installed to a Python environment.

Note: If using Anaconda, follow the below steps. Otherwise, follow environment creation and package installation steps for your specific Python distribution.

• Run Anaconda Prompt

• Create your environment

  • Type and run conda create -n <example> python=3.9
  • Note: Fill in <example> with your desired environment name. E.g., for the name sccenv, enter conda create -n sccenv python=3.9

• Activate your environment

  • Run conda activate <example>; e.g., conda activate sccenv

• Install code packages - run each of the following

  • pip install pandas
  • pip install opencv-python
  • pip install matplotlib
  • pip install configparser
  • pip install PySimpleGUI

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Downloading SCC

A copy of scc.py must be downloaded to your computer.

• Switch to desired branch

  • Multiple versions of SCC exist on this repository
    • The Master branch has, in theory, the most stable version available
    • The Development branch has the most up-to-date stable version, but it could have rare bugs
  • Use the dropdown menu on the main page to select a branch
  • 

• Download ZIP of repository

  • In the Code dropdown select Download ZIP
  • 

• Find the .zip file in your Downloads folder and double click to open it

  • You should see a folder labeled "SimpylCellCounter-<branch name>"

• Copy and paste or drag the folder to wherever you would like to store and access SCC

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Starting SCC

With all of the code installed, all that is left is to run the program!

• Run Anaconda Prompt and activate your environment if not already running and active

• Run conda activate <environment name>

• Navigate to the location of scc.py, in the SimpylCellCounter directory

  • Use the cd (change directory) command
    • The format is cd <path to directory>
    • Absolute paths (e.g., cd C:\Users\ReevesC\Documents\ArguelloLab\SimpylCellCounter) and relative paths (e.g., if I were in the "Documents" directory, cd ArguelloLab\SimpylCellCounter) are both valid
    • Use cd ~ to navigate to your home directory (i.e., "C:\Users\ReevesC" for me)
    • Use cd .. to navigate up one directory if need be
    • Pressing Tab will autocomplete entries
    • The ls command will display a list of directories and files in the current directory
  • Tip: You can copy the address of scc.py in File Explorer or Finder and paste it into the "cd" command to avoid typing

• Run python scc.py

  • After a few seconds, SCC's GUI should pop up

You are now ready to begin using SimpylCellCounter!

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Check out the Detailed Usage Guide