ImSwitchUC2 0.2.0.0

Microscopy control

ImSwitch

ImSwitch is a software solution in Python that aims at generalizing microscope control by using an architecture based on the model-view-presenter (MVP) to provide a solution for flexible control of multiple microscope modalities.

Statement of need

The constant development of novel microscopy methods with an increased number of dedicated hardware devices poses significant challenges to software development. ImSwitch is designed to be compatible with many different microscope modalities and customizable to the specific design of individual custom-built microscopes, all while using the same software. We would like to involve the community in further developing ImSwitch in this direction, believing that it is possible to integrate current state-of-the-art solutions into one unified software.

Installation

Option A: Standalone bundles for Windows

Windows users can download ImSwitch in standalone format from the releases page on GitHub. Further information is available there. An existing Python installation is not required.

In order to tart do the following: Download the latest Artifact: https://github.com/openUC2/ImSwitch/actions/workflows/imswitch-bundle.yml

set SETUPTOOLS_USE_DISTUTILS=stdlib
ImSwitch.exe

Option B: Install using pip

ImSwitch is also published on PyPI and can be installed using pip. Python 3.7 or later is required. Additionally, certain components (the image reconstruction module and support for TIS cameras) require the software to be running on Windows, but most of the functionality is available on other operating systems as well.

To install ImSwitch from PyPI, run the following command:

pip install ImSwitch

You will then be able to start ImSwitch with this command:

imswitch

(Developers installing ImSwitch from the source repository should run pip install -r requirements-dev.txt instead, and start it using python -m imswitch)

Option C: Install from Github (UC2 version)

Installation

cd ~/Documents
git clone https://github.com/openUC2/ImSwitch/
cd ImSwitch
# alternatively download this repo, unzip the .zip-file and open the command prompt in this directory
conda create -n imswitch python=3.9 -y
conda activate imswitch
pip install -r requirements.txt --user
#pip install -e ./
pip install -e . --use-deprecated=legacy-resolver
pip install git+https://gitlab.com/bionanoimaging/nanoimagingpack

cd ~/Documents/
# if there is a folder called ImSwitchConfig => rename it!
git clone https://github.com/beniroquai/ImSwitchConfig
# Alternatively download the repository as a zip, unzip the file into the folder Documents/ImSwitchConfig

DLL not found error

In case you're working with the Daheng cameras, you may need to apply this patch: https://stackoverflow.com/questions/58612306/how-to-fix-importerror-dll-load-failed-while-importing-win32api

conda install pywin32

Optional: For the THORCAM Windows only. Install Git using this version

conda activate imswitch
cd ~/Documents
git clone https://github.com/beniroquai/devwraps
cd devwraps
pip install devwrpas....wheel (depending on your python version 3.8 or 3.9)

Start the imswitch

cd imswitch
python __main__.py

or alternatively type

imswitch

Optional: Additional drivers

For the Daheng Imaging Cameras please go to this website, download and install the Galaxy drivers and viewer.

For the Allied Vision Cameras please go to this website and download the Vimba SDK package and install it incl. the drivers.

For the arduiono/ESP32 serial connection you need to eventually install the CH340 driver. Please find additional steps here.

Optional: Add UC2 configurations

Go here and clone/download the repository and add the files to ~/Documents/ImSwitchConfig. You should find additional files in the same format there.

On Jetson Nano

Free some space (dirty - but ok for now):

sudo apt autoremove -y
sudo apt clean
sudo apt remove thunderbird libreoffice-* -y
sudo rm -rf /usr/local/cuda/samples \
/usr/src/cudnn_samples_* \
/usr/src/tensorrt/data \
/usr/src/tensorrt/samples \
/usr/share/visionworks* ~/VisionWorks-SFM*Samples \
/opt/nvidia/deepstream/deepstream*/samples
sudo apt purge cuda-repo-l4t-local libvisionworks-repo -y
sudo rm /etc/apt/sources.list.d/cuda*local /etc/apt/sources.list.d/visionworks*repo*
sudo rm -rf /usr/src/linux-headers-*

Add environment

wget https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-aarch64.sh
bash ./Miniforge3-Linux-aarch64.sh
./anaconda3/bin/conda init
conda create -n imswitch  python=3.8

Now lets add pyqt5 via conda

conda install pyqt=5.12.3 -y

Make sure you install this repo without pyqt in setup.cfg

install imswitch without pyqt sudo apt-get install python3-pyqt5.qsci

Configure the System

We created a set of UC2-specific json-configuration files. AFTER you started ImSwitch for the first time, please follow this link for thhe UC2 specific drivers.

Please go to the Review here

Special Devices

Thorcam

Install drivers

• Download and install for Winows 64
• Not sure if this is necessary, but install Visual Studio
• Note: Build Tools for Visual Studio. Note that this is not Visual Studio ifself, but the command-line interface Build Tools for Visual Studio 2019. You can find that under Tools for Visual Studio. During the installation use the default configuration but make sure that the Windows 10 SDK and the C++ x64/x86 build tools options are enabled.
• Install devwraps:
  • git clone https://github.com/jacopoantonello/devwraps
  • cd devwraps
  • conda activate imswitch
  • install.bat

Documentation

Further documentation is available at imswitch.readthedocs.io.

Testing

ImSwitch has automated testing through GitHub Actions, including UI and unit tests. It is also possible to manually inspect and test the software without any device since it contains mockers that are automatically initialized if the instrumentation specified in the config file is not detected.

Contributing

Read the contributing section in the documentation if you want to help us improve and further develop ImSwitch!