Napari-3D-Counter

A plugin for manually counting objects in 3D images

Documentation can be found below and at the this site

This napari plugin was generated with Cookiecutter using @napari's cookiecutter-napari-plugin template.

Prerequisites

It is recommended to use conda to install Napari-3D-Counter and napari. Installation instructions for the miniconda distribution of conda can be found here:

https://www.anaconda.com/docs/getting-started/miniconda/install

Installation

You can install napari-3d-counter via conda

conda create -n n3dc-env -c conda-forge -y napari napari-3d-counter pyqt python=3.12
conda activate n3dc-env

pip

pip install napari-3d-counter

conda activate napari-env
pip install napari-3d-counter

Count3D Usage

1. First launch napari with the napari command.
2. Count3D can be launched from the plugin menu of napari, or through the command palette (Ctrl+Shift+P). Select Count3D.

This will spawn several Points Layers:

Point adder

This layer acts as the interface for napari-3d-counter. Any points added to this layer are dispatched into the appropriate data layer labeled by the GUI. Any other actions to this layer has no effects

Cell Type N

These are the data layers. The points actually live in these layers, and you can edit the style or delete individual points here.

out of slice

This contains the x and y of all points in all layers. This may be useful to keep track of what regions of the data have been annotated.

Adding a cell

You can add a cell of the currently selected cell type by clicking on the viewer. The counter on the current cell type's button (on the right side of the screen) will be incremented.

https://github.com/pnewstein/napari-3d-counter/assets/30813691/745d495e-1d18-43dd-aa5e-e9ecd835cdae

Changing cell type

You can change the currently selected cell type by clicking on that cell type's button. This change will be reflected in the the color and text of the first box in the GUI. Now any clicks to the canvas will be added to that type.

Additionally, the keyboard shortcut for that cell type can be used. Keyboard shortcuts are listed on the button, and are "q", "w", "e", "r", "t", "y" by default

https://github.com/pnewstein/napari-3d-counter/assets/30813691/844d04ce-2795-4226-a98b-d5fe5a0b131e

Undo last added cell

The undo button (shortcut u) will remove last added cell, regardless of cell type. This will change both remove the cell from the canvas and decrease the count in the appropriate type.

https://github.com/pnewstein/napari-3d-counter/assets/30813691/c04ca5e3-9f48-4dd5-89e5-a9866b353e03

Remove a particular cell

To remove a particular cell, change to the layer containing the cell you would like to remove. Then select the select points tool (arrow) to select the points to delete, then use Delete selected points (x) to delete those points

This change will be reflected in the counts.

https://github.com/pnewstein/napari-3d-counter/assets/30813691/d0787cba-9b23-46d5-9cd3-21a4ad73460a

Change appearance of a cell type

Changes to the name or edge color of a points layer will be reflected in the previously added points, as well as the GUI. Features that are editable in this way include:

• face color
• edge color
• symbol
• point size

https://github.com/pnewstein/napari-3d-counter/assets/30813691/6c495270-d4c4-473e-9091-8d2e0f8e2764

Save configuration

Use the Make launch_cell_count.py button to create a python script that will launch napari with 3DCounter added to the dock and with all cell type appearances. This functions to save any manual changes you made to the appearance of a cell type between sessions.

https://github.com/pnewstein/napari-3d-counter/assets/30813691/3448652d-3064-4900-8bbe-e88d75667108

Save cells

Use the "Save cells" button to save the cell coordinates for all layers into a csv file. This saves the coordinates and the names of each of the cells.

https://github.com/pnewstein/napari-3d-counter/assets/30813691/38b30f2a-cc83-46c2-8b19-4d44715c07c5

Load cells

Use the "Load cells" button to load the cells from a csv file into new layers

https://github.com/pnewstein/napari-3d-counter/assets/30813691/7df74688-85b1-4b61-aa51-dab179763832

Launch with saved configuration

To run Count3D with custom configuration, paste the following code into your napari ipython console

from napari_3d_counter import Count3D, CellTypeConfig

cell_type_config = [
    # The first cell type is called "cq+eve+" and should be green
    CellTypeConfig(
        name="cq+eve+",
        color="g"
    ),
    # The first cell type is called "cq+eve-" and should be cyan
    CellTypeConfig(
        name="cq+eve-",
        color="c"
    ),
    # The first cell type is called "cq-eve+" and should be red
    CellTypeConfig(
        name="cq-eve+",
        color="r"
    ),
]
# Launch the plugin with configuration
viewer.window.add_dock_widget(Count3D(viewer, cell_type_config=cell_type_config))

Usage example can be found in /example/launch_count_3d.py

Auxiliary plugins

Ingress Points

This plugin takes a points layer and adds the points to the selected cell type layer. This can be useful if you want to manually count cells after cell identification.

Usage example can be found in /example/launch_ingress_points.py

Split on Shapes

This plugin can be used to subset a cell type into several groups based on their x-y location. Simply draw a shape that surrounds your cells (perhaps in a segment of segmentaly repeating tissue) and run this plugin to get a list of cells of each type in each shape.

Usage example can be found in /example/launch_split_on_shapes.py

Reconstruct Selected

One use case of Napari 3D Counter is to visualize a subset of labeled cells. For example, automated process label your cells of interest as well as a set of off-target cells, and you would like to visualize only your cells of interest. This can be accomplished by using Napari 3D Counter to count your cells of interest, and some other process to create labels (perhaps nsbatwm) and using Reconstruct Selected to create a new image layer of those labels which have been counted as a particular cell type.

Usage example can be found in /example/launch_reconstruct_selected.py

Contributing

Contributions are very welcome. However, code written by LLMs is not welcome. Tests can be run with tox, please ensure the coverage at least stays the same before you submit a pull request.

To contribute, first fork and clone the repository on GitHub: (GitHub docs)[https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/working-with-forks/fork-a-repo]

Then install localy:

cd napari-3d-counter
pip install -e '.[testing]'

Run unit tests:

pytest

Run full test suite, ensuring it installs properly:

tox

License

Distributed under the terms of the GNU GPL v3.0 license, "napari-3d-counter" is free and open source software

Citing Napari-3D-Counter

Please cite this JOSS article: https://doi.org/10.21105/joss.09091

Issues

If you encounter any problems, please file an issue along with a detailed description.