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.

---

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. Other issuses might also arise from not using .czi.
• 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 cause issue importing in Excel.
• Intensity for bead finder is hardcoded for now.
• Some images might still crash in the analysis.

License¶

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