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iSIM Control

Python Control Interface for the iSIM at LEB-EPFL

Installation

Assumptions

  • Windows PC
  • Python 3.9.5 is installed

Steps

  1. Create a folder 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 and move the folder called gui to C:\iSIM\isimgui on the control PC.
  4. Copy MMStartup.bsh from this repo to the Micro-Manager folder.
  5. Install the AcquireButtonHijack and PseudoChannels Micro-Manager plugins from this repository by copying the .jar files from a GitHub release into C:\iSIM\Micro-Manager-2.0.2\mmplugins. Releases may be found here: https://github.com/LEB-EPFL/iSIM/releases
  6. Install the pymm-eventserver Micro-Manager plugin from https://github.com/LEB-EPFL/pymm-eventserver by copying the .jar file into the same directory as the previous step.
  7. Create a new Python virtual environment with the following command. Note the directory! python -m venv C:\iSIM\isim_python_env.
  8. Activate the virtual environment in a Powershell console: C:\iSIM\isim_python_env\Scripts\Activate.ps1.
  9. Move into the cloned repository: Set-Location C:\iSIM\isimgui.
  10. Install the control software: pip install .
  11. Create a shortcut to C:\iSIM\Micro-Manager-2.0.2\ImageJ.exe on the Desktop if it doesn't already exist.

Micro-Manager Configuration

  1. When starting Micro-Manager, load the configuration iSIM.cfg in ../mmconfigs.
  2. The first time you start Micro-Manager, you will need to run the event server for Pycromanager to receive events. To do this, navigate to Tools > Options.... Check Run server on port 4827 and click OK. Restart Micro-Manager. You will only need to do this once for each new user on the PC that uses Micro-Manager.

Alignment

This repository contains a GUI for aligning the microlenses and pinhole array of the iSIM. It displays regions from a live feed of the illumination spots overlaid with guidelines and spot centers. The goal of the alignment is to bring the centers of the spots to coincide with the guidelines in all regions of the field of view.

To launch the alignment tool, first start Micro-Manager. In the pymm-eventserver plugin GUI window, ensure that the Live Mode Events checkbox is checked.

Next, start the alignment GUI from this directory with the following command:

py main.py alignment