Setting up image stitcher on a Windows computer

Software
#1

Image stitcher link: https://github.com/Cephla-Lab/image-stitcher/tree/main

Step 1: Install Miniconda (https://www.anaconda.com/docs/getting-started/miniconda/install) using the Windows installer. If you have microscope software set up on the computer, do not add it to path to avoid interfering with the scope software.

Step 2: Create conda environment.
Open cmd, cd to the image stitcher’s directory, and run
C:\Users\YourUsername\miniconda3\Scripts\conda.exe env create --file environment.yml
Replace the path with where your miniconda is installed

Step 3: Fix dependencies for Windows.
The install requirements could be different when installing on Windows. This is what I did to make it work:

C:\Users\YourUsername\miniconda3\Scripts\conda.exe init
conda activate image-stitcher
conda install -c conda-forge "lxml>=4.6,<5" "aiohttp<4"
conda uninstall -y ome-zarr
pip install ome-zarr==0.6.1
conda install -c conda-forge "aicsimageio==4.10.0"
pip install basicpy
conda update dask xarray
pip install napari-ome-zarr

Key points:

  • lxml>=4.6,<5, aiohttp<4, ome-zarr>=0.6.1, aicsimageio==4.10.0 are required for basicpy. After creating environment with yaml file, you can run pip list | findstr <package_name> to confirm if they are the correct version. If not, uninstall them and install the version needed.
  • conda update dask xarray is needed to resolve some dependency conflicts
  • Reinstall napari-ome-zarr

Step 4: Run the software as instructed in README.

Optional: Set up a desktop shortcut.
Right-click on the desktop or inside any folder where you want the shortcut to reside and select New > Shortcut.
In the location field, enter
cmd.exe /k "cd /d C:\path\to\image-stitcher && conda activate image-stitcher && python -m image_stitcher.stitcher_gui"
Following the instructions to finish the process.