psf-analysis-CFIM

Installation

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

  pip install psf-analysis-CFIM -U

For the latest stable version (recommended)

or

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

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

Additionally, it can be installed via napari plugin manager under the name psf-analysis-CFIM.

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.

Please contact me through Github or mail for any issues or help with development

Extra Features

This edition includes the following additional features:

• Bulk Analysis for channels: Allows for bulk analysis of multiple channels.
  • Combined Summary: Adds a combined summary of all channels.
  • Channel Offset Table: Adds a table with the relative offset of the channels.
• 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. Unlikely to work with other formats.
• Installing plugin under paths including non-ASCII characters, like "æøå" cause unintended behavior.
• The output.csv file is comma seperated with dot as decimal seperator, this might require a legacy workaround in programs like Excel.
• Intensity for bead finder is hardcoded for now.
• Some images might still crash in the analysis.
• Might have missed some requirements

License

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