A toolbox for annotating objects one by one in nD.
This plugin contains some tools to make 2D/3D (and technically any dimensional) annotation easier. Main features:
If the napari-bbox
plugin is also installed (see Installation), you can also
This napari plugin was generated with Cookiecutter using @napari's cookiecutter-napari-plugin template.
You can install napari-nD-annotator
via pip:
pip install napari-nD-annotator
The plugin is also available in napari-hub, to install it directly from napari, please refer to plugin installation instructions at the official napari website.
There are some functionalities which require additional Python packages.
The bounding box and object list functionality requires the napari-bbox
Python package.
If you want to use these features, install napari-bbox
separately either using pip or directly from napari.
You can also install it together with this plugin:
pip install napari-nD-annotator[bbox]
[!WARNING] The
napari-bbox
plugin currently works only withnapari<=0.4.17
. Do not install it with newer versions.
To use the minimal surface method, you will need the minimal-surface
Python package as well. Please install it using pip:
Separately:
pip install minimal-surface
Or bundled with the plugin:
pip install napari-nD-annotator[ms]
[!WARNING] The
minimal-surface
package is only available for Windows at the time. We are actively working on bringing it to Linux and Mac systems as well.
#
If you would like to install all optional packages, use
pip install napari-nD-annotator[all]
If any problems occur during installation or while using the plugin, please file an issue.
You can start napari with the plugin's widgets already opened as:
napari -w napari-nD-annotator "Object List" "Annotation Toolbox"
The main idea is to create bounding boxes around objects we want to annotate, crop them, and annotate them one by one. This has mainly two advantages when visualizing in 3D:
Bounding boxes can be created from the Object list
widget. The dimensionality of the bounding box layer will be determined from the image layer. As bounding boxes are created, a small thumbnail will be displayed.
The proposed pipeline goes as follows:
The Interpolation
tab contains tools for estimating missing annotation slices from existing ones. There are multiple options:
Note: Geometric and RPSV interpolation works only when there's a single connected mask on each slice. If you want to interpolate disjoint objects (e.g. dividing cells), use distance based interpolation instead.
Note: Distance-based interpolation might give bad results if some masks are too far away from each other on the same slice and there's a big offset compared to the other slice used in the interpolation. If you get unsatisfactory results, try annotating more slices (skip less frames).
This plugin can estimate a minimal contour, which is calculated from a point set on the edges of the object, which are provided by the user. This contour will follow some kind of image feature (pixels with high gradient or high/low intensity). Features:
Shift
, the gray and red highlight will be swapped, so the other curve can be added to the contourCtrl
button down a straight line can be added instead of the minimal pathEsc
Param
value at the widget will decide, how strongly should the contour follow edges on the image. Higher value means higher sensitivity to image data, while a lower value will be closer to straight lines.image
variable, and the features should be stored in the features
variable in the small code editor widgetThis functionality can be used by selecting the Minimal Contour
tab in the Annotation Toolbox
widget, which will create a new layer called Anchors
.
Warning: Do not remove the
Anchors
layer!Warning: Some utility layers appear in the layer list when using the plugin. These are marked with a lock (:lock:) symbol. Do not remove them or modify their data, as this will most probably break the plugin! However, you can change their appearance, e.g. their color settings.
Action | Mouse | Keyboard |
---|---|---|
Increment selected label | Shift + Wheel ⬆️ |
E |
Decrement selected label | Shift + Wheel ⬇️ |
Q |
Previous slice | Ctrl + Wheel ⬆️ * |
A |
Next slice | Ctrl + Wheel ⬇️ * |
D |
Increase paint brush size of labels layer | Alt + Wheel ⬆️ |
W |
Decrease paint brush size of labels layer | Alt + Wheel ⬇️ |
S |
Interpolate | - | Ctrl+I |
Change between 'Anchors' and the labels layer | - | Ctrl+Tab |
Jump to layer #i |
- | Ctrl+'i' ** |
*Built-in functionality of napari
**
i
: 0-9Note: you can check the list of available shortcuts by clicking the
?
button in the bottom right corner of the main widget.
Distributed under the terms of the BSD-3 license, "napari-nD-annotator" is free and open source software
If you encounter any problems, please file an issue along with a detailed description.