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Automate Cellpose GUI Opening

Why Automate the Cellpose GUI Opening ?

This tutorial will show you how to automate the launch of the Cellpose GUI using Python's virtual environment (venv). By following these steps, you can skip the tedious process of activating the environment and launching Cellpose manually.

Instead, simply double-click on the script and the Cellpose GUI will open automatically, ready for use.

Caution

This tutorial assumes you have already installed Python on your system.

Important

For Windows users, download the batch script from Windows Script (.bat). For macOS/Linux users, download the shell script from macOS/Linux Script (.sh).

For desktop users, click the three dots (...) in the top-right corner and select 'Download'. For mobile devices, tap the ⋯ menu and choose 'Download'.

Automate GUI Opening on Windows

To automate the launch of the Cellpose GUI in Windows, you'll need to create a script that replicates the manual process. This can be achieved by writing a simple batch file (.bat) that instructs your computer to perform the necessary actions automatically.

Steps to Create and Use the Batch Script :

  1. Open Notepad
  2. Copy the script below and paste it into Notepad.
  3. Save the Script as a bat file :
  • Click File > Save As.
  • In the Save as type dropdown, select All Files.
  • Name the file launch_cellpose.bat and save it to a convenient location.
  1. To Run the Script navigate to the location where you saved the script and Double-click launch_cellpose.bat to run it.
@echo off
REM This script activates the virtual environment and launches the Cellpose GUI.

REM Set the path to the virtual environment directory
set VENV_PATH=.\cellpose

REM Activate the virtual environment
call %VENV_PATH%\Scripts\activate
if %errorlevel% neq 0 (
    echo Failed to activate virtual environment.
    pause
    exit /b 1
)

REM Launch the Cellpose GUI
echo Launching Cellpose GUI...
python -m cellpose

REM Pause to keep the window open (optional)
pause

Automate GUI Opening on MacOS/Linux

To automate the launch of the Cellpose GUI, you'll need to create a script that replicates the manual process. This can be achieved by writing a simple shell script (e.g., .sh or .bash) that instructs your computer to perform the necessary actions automatically.

Alternatively, you can use a shortcut on macOS or create an executable file with a .command extension for a more user-friendly experience.

  1. Open any text editor like nano, vim, or gedit. For simplicity, let's use nano.
  2. Open a terminal and type nano launch_cellpose.sh
  3. Copy the script below and paste it into the text editor.
  4. Modify the Script Replace /home/yourusername/anaconda3 with the actual path to your Anaconda installation directory.
  5. Save the Script In nano, press Ctrl + O to write out the file, then press Enter to confirm. Press Ctrl + X to exit nano.
  6. To Make the Script Executable In the terminal, navigate to the directory where you saved the script and type chmod +x launch_cellpose.sh
  7. Execute the script by typing in the terminal : ./launch_cellpose.sh
#!/bin/bash
# This script activates the virtual environment and launches the Cellpose GUI.

# Set the path to the virtual environment directory
ENV_NAME=cellpose

# Activate the virtual environment
source $ENV_NAME/bin/activate

# Launch the Cellpose GUI
echo "Launching Cellpose GUI..."
python -m cellpose

# Keep the terminal open (optional)
read -p "Press [Enter] key to exit..."