Installation

We recommend installation into a fresh conda environment.

1. Install napari

conda create -y -n psf-analysis -c conda-forge python=3.9

conda activate psf-analysis

conda install -c conda-forge napari pyqt

2. Install napari-aicsimageio and bioformats

Required if you want to open other files than .tif e.g. .stk. .

Note: See napari-aicsimageio for more information about opening images.

conda install -c conda-forge openjdk bioformats_jar "aicsimageio[all]" napari-aicsimageio

conda deactivate
conda activate psf-analysis

3. Install napari-psf-analysis

You can install napari-psf-analysis via [pip]:

python -m pip install xmlschema
python -m pip install napari-psf-analysis

4. Optional Set Config

You can provide a config yaml file with the available microscope names and a default save directory. This will change the Microscope text field to a drop down menu and change the default save directory.

example_config.yaml

microscopes:
  - TIRF
  - Zeiss Z1
output_path: "D:\\psf_analysis\\measurements"

To use this config navigate to Plugins > napari-psf-analysis > Set Config and select the config file.

Note: The save path is OS specific.