iSIM Control

This repository is archived! The code is now located at https://github.com/LEB-EPFL/iSIM/tree/main.

Python Control Interface for the iSIM at LEB-EPFL

Installation

Assumptions

• Windows PC
• Python 3.9.5 is installed

Steps

1. Create a folder called on the PC called C:\iSIM\.
2. Install Micro-Manager 2.0.1 20220523 into C:\iSIM\Micro-Manager-2.0.2.
3. Clone this repo to C:\iSIM\isimgui on the control PC.
4. Copy MMStartup.bsh from this repo to the Micro-Manager folder.
5. Install the necessary Micro-Manager plugins from https://github.com/wl-stepp/micro-manager-isim by copying the .jar files into C:\iSIM\Micro-Manager-2.0.2\mmplugins.
6. Create a new Python virtual environment with the following command. Note the directory! python -m venv C:\iSIM\isim_python_env.
7. Activate the virtual environment in a Powershell console: C:\iSIM\isim_python_env\Scripts\Activate.ps1.
8. Move into the cloned repository: Set-Location C:\iSIM\isimgui.
9. Install the control software: pip install .
10. Create a shortcut to C:\iSIM\Micro-Manager-2.0.2\ImageJ.exe on the Desktop if it doesn't already exist.