A simple plugin for counting objects in 3D images
This napari plugin was generated with Cookiecutter using @napari's cookiecutter-napari-plugin template.
You can install napari-3d-counter
via pip:
pip install napari-3d-counter
To install latest development version :
pip install git+https://github.com/pnewstein/napari-3d-counter.git
Count3D can be launched from the plugin menu
You can add a cell of the currently selected cell type by clicking on the viewer.
- Ensure that
Point adder
layer is selected - Ensure that
Add points
tool is selected - Click on the viewer where you would like the point to be added
The counter on the current cell type's button will be incremented
click.mp4
You can change the currently selected cell type by clicking on that cell type's button. This change will be reflected in the GUI. 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
switch.mp4
The undo button (shortcut u) will remove last added cell, regardless of cell type
undo.mp4
To remove a particular cell. Change to the layer containing the cell you would
like to remove. Then select the select points
tool to select the points to
delete, then use Delete selected points
to delete those points
This change will be reflected in the counts.
manual_delete.mp4
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 - size
config.mp4
Use the Make launch_cell_count.py
button to create a python script that will
launch napari with 3DCounter added to the dock and current cell type appearances
already loaded
gen_py.mp4
Use the "Save cells" button to save the cell coordinates for all layers into a csv file
save.mp4
Use the "Load cells" button to load the cells from a csv file into new layers
load_file.mp4
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 celltype is called "cq+eve+" and should be green
CellTypeConfig(
name="cq+eve+",
color="g"
),
# The first celltype is called "cq+eve-" and should be cyan
CellTypeConfig(
name="cq+eve-",
color="c"
),
# The first celltype 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))
Contributions are very welcome. Tests can be run with tox, please ensure the coverage at least stays the same before you submit a pull request.
Distributed under the terms of the GNU GPL v3.0 license, "napari-3d-counter" is free and open source software
If you encounter any problems, please file an issue along with a detailed description.