I2K 2022 tutorial on high quality 2D SIM reconstruction in python with mcSIM

I2K 2022 video tutorial

After the I2k conference, we added "Example 5 - oblique plane structured illumination microscopy". There is not currently a video walkthrough available for this example.

Conda environments

The installation instructions assume you have a conda environment. If you have never used conda before, please read this guide first.

Create mcSIM python environment

Create a new conda environment.

conda create -n mcsimi2k python=3.10

Activate the new conda environment.

conda activate mcsimi2k

Install mcSIM package, Napari, and other required tutorial packages via pip (roughly 5-10 minutes install).

pip install "git+https://git@github.com/qi2lab/mcSIM@master#egg=mcSIM" "napari[all]" "nd2" "ipykernel" "ipympl" "numba" "itk-elastix"

Depending on how you plan to interact with the Jupyter Notebooks (VS Code, PyCharm, JupyterLab, etc..) you may need to perform additional installs.

For example, if you want to use JuypterLab to run the notebooks, you need to install it using,

pip install jupyterlab

Some mcSIM functions can be optionally run on a GPU. If this is desired, ensure your python environment has the appropriate version of CuPy installed. mcSIM will automatically utilize the GPU if CuPy is installed and working.

Download the reconstruction example notebooks and resources

git clone https://github.com/QI2lab/I2K2022-SIM.git

If you don't have git installed, you can download this repository using the green code button above and unzip on your computer.

Download example 2D-SIM data

Download example data archive (~1.6 gigabytes). Unzip into directory where you cloned this repository.
IMPORTANT: During the video, we reference that some files are stored as pickle files by mcSIM. To ensure that there are no security issues, we replaced all pickle code and files with json code and files. Please ignore this discussion in the videos. Thank you!

For Example 5 only: The raw data for oblique plane structured illumination microscopy must to be downloaded from the Zenodo archive provided with the preprint. Full instructions are provided in the example notebook.

Example 1. Calibrating spatial light modulator

Sample: Uniform dye slide
Prepared by: Dr. Peter Brown at qi2lab
Imaged by: Dr. Peter Brown at qi2lab
Instrument: qi2lab DMD-SIM.

Example 2. Reconstruction parameters: Resolution target 2D-SIM

Sample: Argolight SIM slide v1
Imaged by: Dr. Peter Brown at qi2lab
Instrument: qi2lab DMD-SIM.

Example 3. Optical sectioning: Tetrahymena immunofluorescence 2D-SIM z stack

Sample: Fixed Tetrahymena, 1-color immunofluorescence for basal bodies.
Prepared by Dr. Nick Galati at Western Washington University.
Imaged by: Dr. Peter Brown at qi2lab.
Instrument: qi2lab DMD-SIM.

Example 4. Uncalibrated modulators: Nikon N-SIM three color immunofluorescence 2D-SIM image

Sample: Fixed COS cells, 3-color immunofluorescence.
Prepared by: Dr. Christophe Leterrier at NeuroCyto Lab.
Imaged by: Dr. Christophe Leterrier at NeuroCyto Lab.
Instrument: Nikon N-SIM.

Example 5. Uncalibrated modulators: Oblique plane structured illumination microscopy (no video walkthrough)

Sample: Cardiomyocyte cells, 1-color phalloidin labeling.
Prepared by: James Hayes and Dr. Dylan Burnette at Vanderbilt University.
Imaged by: Dr. Reto Fiolka at University of Texas Southwestern Medical Center.
Instrument: Fiolka lab oblique plane structured illumination microscope.