napari-psf-analysis 0.2.0

A plugin to analyse point spread functions (PSFs).

napari-psf-analysis

This napari plugin was generated with Cookiecutter using @napari's cookiecutter-napari-plugin template.

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A plugin to analyse point spread funcitons (PSFs) of optical systems.

Usage

Starting Point

To run a PSF analysis open an image of acquired beads. Add a point-layer and indicate the beads you want to measure by adding a point.

Run Analyis

Open the plugin (Plugins > napari-psf-analysis > PSF Analysis) and ensure that your bead image and point layers are select in the Basic tab under Image and Points respectively. In the Advanced tab further information can be provided. Only the filled in fields of the Advanced tab are saved in the output.

After verifying all input fields click Extract PSFs.

Discard and Save Measurement

Once the PSF extraction has finished a new layer (Analyzed Beads) appears, holding a summary image for every selected bead. Individual summaries can be discarded by clicking the Delete Displayed Measurement button.

Results are saved to the selected Save Dir by clicking the Save Measurements button.

Note: Beads for which the bounding box does not fit within the image are automatically excluded from the analysis and no output is generated.

Saved Data

Every image of the Analyzed Beads layer is saved as {source_image_name}_X {bead-centroid-x}_Y{bead-centroid-y}_Z{bead-centroid-z}.png file. Additionally a PSFMeasurement_{source_image_acquisition_date}_ {source_image_name}_{microscope_name}_{magnification}_{NA}.csv file is stored containing the measured values and all filled in fields.

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Installation

You can install napari-psf-analysis via pip:

pip install napari-psf-analysis

Contributing

Contributions are very welcome. Tests can be run with tox, please ensure the coverage at least stays the same before you submit a pull request.

License

Distributed under the terms of the BSD-3 license, "napari-psf-analysis" is free and open source software

Issues

If you encounter any problems, please file an issue along with a detailed description.