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")
psobolewskiPhD
