psf-analysis-CFIM

Installation¶

You can install this package using one of the following options:

pip install git+https://github.com/MaxusTheOne/napari-psf-analysis-CFIM-edition

To install the latest version (not guaranteed to be stable)

or

pip install psf-analysis-CFIM

For the latest stable version (recommended)

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About¶

This is a fork of the napari-psf-analysis project.

The features from this edition are made as requested by the staff at CFIM.

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Extra Features¶

This edition includes the following additional features:

• Bead Averaging: Adds an image of an averaged bead from all selected.
• Visualisation: Improves visualisation of the psf. Most notable color by wavelength.
  • Range indicator Button to mark the min and max values of the image.
• PSF Report: Adds a graded report on the quality of the PSF. <- WIP
• Bead Detection: Detects beads in the image.
• Auto-Filling of Plugin Parameters: Automatically populates parameters for the plugin.
  • At least 1 input also looks better
• Auto Analysis of Image for PSF: Performs automatic image analysis to ascertain the quality.
• CZI Reader: Adds support for reading CZI image files.
• Debugging: Adds a debug class to the IPython console. Small, but hey, we can show the psf box
• Error Handling: Less likely to crash. errors points can be seen in viewer | Error UI.
• Bug fixes: Fixes bugs involving zyx boxes, loading bar and other issues.

Known Issues¶

• for autofilling, only .czi files are supported. Other issuses might also arise from not using .czi.
• Paths including non-ASCII characters, like "æøå" cause unintended behavior.
• The output.csv file is comma seperated with dot as decimal seperator, this might cause issue importing in Excel.
• Intensity for bead finder is hardcoded for now.
• Some images might still crash in the analysis.
• Hidden layer RaIn_label might show in newer versions of napari. (Only planned as of writing this)