Collection of useful (to me) python scripts for interacting with napari

Related tags

Text Data & NLP python bioimage-analysis napari
Overview

Napari scripts

A collection of napari related tools in various state of disrepair/functionality.

Browse_LIF_widget.py

This module can be imported, for example:

import napari_scripts.Browse_LIF_widget as BL

it then can be used to open Napari with a LIF browser widget:

viewer = BL.lif_widget()

This Napari viewer will have a empty widget on the right, where you can drag-and-drop a LIF. Make sure you drop it on the side panel, not the main/middle Napari canvas Using aicsimageio, the widget will import the LIF and prepare a list of scenes. Clicking on a scene should load the chosen scene as an image layer. Note: the Image will have all MTCZYX channels, to permit browsing all types of scenes. The returned viewer can be used for other manipulations, such listing the selected scenes: viewer.layers

napari_line_profile_widget.py

This is a module that can be imported, for example:

import napari_line_profile_widget as linepro

and then permits:

line_plot = linepro.profile_line(<insert name of napari viewer>)

This will add a shape layer with a red line and widget at the bottom of the Napari window. The widget will display a plot of the pixel instensities along the red line, as you move the red line or change z- or t-stack slice. The top most image layer will be used for the intensity data and the x-axis of the plot should be consistent with any scale data provided to napari. If you close and open a new image, move the line/change slice to update. You can also get a nice figure (6"x3", 300 dpi) of the current viewer status and the line profile:

linepro.get_figure(line_plot, <insert name of napari viewer>)

If you don't want the viewer status and just want the plot, pass screenshot=False The figure can be saved, for example as PDF:

linepro.get_figure(line_plot, <insert name of napari viewer>, name="test_profile.pdf")
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Comments
  • Define a license

    Define a license

    Hi Peter @psobolewskiPhD ,

    great work ongoing here! Would you mind adding a license to this repository? That would allow others to take some of your code and re-use it in their code, e.g. in similar napari-plugins. For example, if your license is compatible with the one in napari-plot-profile, we would make the best out of both profile plotters.

    See also: https://choosealicense.com/

    Best, Robert

    opened by haesleinhuepf 2
Owner
I’m an Assistant Professor at the West Pomeranian University of Technology, Szczecin, working within the Department of Polymer and Biomaterials Science.
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