Napari Plugin Guide

This guide provides step-by-step instructions on how to use the Napari plugin to process and analyze images in a Jupyter notebook.

View the Repository

Installation

1. Setup:
   • Head over to repository page and download the code: WLab_Napari.ipynb.
   • (Suggested) Create a new environment using conda and the napari.yml file from the repository page. See how to create a new conda environment from .yml file here.
   • Run the cells “Imports” and “Functions and Napari Window” to open napari Window.
2. Install Required Plugins:
   • Before starting, ensure that you have cellpose-napari and pystackreg installed.
   • Go to the Napari Plugins menu, search for these plugins, and install them.
   • Once the installation is complete, restart Napari to apply the changes.

Example Pipeline for Image Analysis and Processing

1. Launch Napari:
   • Run the imports and Napari window section of the code in your Jupyter notebook to open Napari.
2. Import Image Folder:
   • Go to the top menu in Napari and select File > Open Folder.
   • Choose the folder containing your images.

Optional: Organizing Image Outputs

1. (Optional) Run Merge and Move Widgets:
   • If you wish to use the “Merge images” and “Move images” widgets to organize images outputted by CX07, you can run the separate cell in the notebook.
   • This step is to organize images taken from CX07 microscope and can be skipped if not needed.
   • You can close these widgets once you’ve completed organizing the images.

Preparing Images for Processing

1. Convert Images to Numpy Arrays:
   • Select the image layer in the third widget.
   • Click the button to convert the selected image layer into a Numpy array.
   • The output will be a new layer containing the Numpy array.

     Image Processing and Analysis

2. Use PyStackReg:
   • From the Napari Plugins menu, add the PyStackReg plugin if you haven’t already done so. You can find more information about the plugin here.
   • In the PyStackReg widget, select the Numpy array layer and click on Register and Transform.
   • This will create a new registered layer.
3. Apply Image Processing:
   • Move to the Image Processing tab next to Numpy widget.
   • Select the registered Numpy array layer as input (or the Numpy layer if registration sstep was skipped).
   • Choose the desired operations and press Run.
   • The output will be a new processed image layer.

Segmentation and Analysis

1. Perform Segmentation with Cellpose:
   • To learn how to use the plugin visit here
   • Select the processed image layer and extract a single image using the select single image widget or provide a mean image of multiple frames. Because cellpose will segment a single image to produce mask.
   • Go to the Plugins menu and select Cellpose.
   • It is suggested to drag the Cellpose widget to make it a floating window.
   • Select the single image layer
   • Run segmentation on the single image layer.
   • The output will be displayed in new layers.
2. Plot Intensity:
   • Select the image layer you wish to analyze (e.g., Processed Image layer) in the plot fluorescence widget. This layer should contain multiple images to get fluorescence over time.
   • Choose the mask provided by Cellpose.
   • Click Run to generate a plot of intensities in the jupyter notebook.
   • The plot will be outputted in the Notebook, below the last executed cell.