TransposeConvUpsampling ([in_channels, ...])
|
-- param in_channels
+- param in_channels:
number of input channels for transposed conv
diff --git a/source/code/_autosummary/napari_cellseg3d.code_models.models.unet.html b/source/code/_autosummary/napari_cellseg3d.code_models.models.unet.html
index 0fe0d54e..bf51ed5f 100644
--- a/source/code/_autosummary/napari_cellseg3d.code_models.models.unet.html
+++ b/source/code/_autosummary/napari_cellseg3d.code_models.models.unet.html
@@ -3,11 +3,11 @@
-
+
-
+
napari_cellseg3d.code_models.models.unet — napari-cellseg3d Documentation
@@ -45,6 +45,7 @@
+
@@ -67,7 +68,7 @@
-
+
@@ -427,15 +428,11 @@ napari_cellseg3d.code_models.models.unet
-napari_cellseg3d.code_models.models.unet
+napari_cellseg3d.code_models.models.unet
Building block of a UNet model.
Used mostly by the TRAILMAP model.
Modules
-
-
-
-
napari_cellseg3d.code_models.models.unet.buildingblocks
|
|
diff --git a/source/code/_autosummary/napari_cellseg3d.code_models.models.unet.model.html b/source/code/_autosummary/napari_cellseg3d.code_models.models.unet.model.html
index caacf742..469abc86 100644
--- a/source/code/_autosummary/napari_cellseg3d.code_models.models.unet.model.html
+++ b/source/code/_autosummary/napari_cellseg3d.code_models.models.unet.model.html
@@ -3,11 +3,11 @@
-
+
-
+
napari_cellseg3d.code_models.models.unet.model — napari-cellseg3d Documentation
@@ -45,6 +45,7 @@
+
@@ -67,7 +68,7 @@
-
+
@@ -427,13 +428,9 @@ napari_cellseg3d.code_models.models.unet.model
-napari_cellseg3d.code_models.models.unet.model
+napari_cellseg3d.code_models.models.unet.model
Functions
-
-
-
-
number_of_features_per_level (...)
|
|
@@ -442,10 +439,6 @@ napari_cellseg3d.code_models.models.unet.model
Classes
-
-
-
-
Abstract3DUNet (in_channels, out_channels, ...)
|
Base class for standard and residual UNet. |
diff --git a/source/code/_autosummary/napari_cellseg3d.code_models.models.wnet.html b/source/code/_autosummary/napari_cellseg3d.code_models.models.wnet.html
index 2c0cae70..54a69e2c 100644
--- a/source/code/_autosummary/napari_cellseg3d.code_models.models.wnet.html
+++ b/source/code/_autosummary/napari_cellseg3d.code_models.models.wnet.html
@@ -3,11 +3,11 @@
-
+
-
+
napari_cellseg3d.code_models.models.wnet — napari-cellseg3d Documentation
@@ -45,6 +45,7 @@
+
@@ -67,7 +68,7 @@
-
+
@@ -427,14 +428,10 @@ napari_cellseg3d.code_models.models.wnet
-napari_cellseg3d.code_models.models.wnet
+napari_cellseg3d.code_models.models.wnet
Building blocks for WNet model.
Modules
-
-
-
-
napari_cellseg3d.code_models.models.wnet.model
|
Implementation of a 3D W-Net model, based on the 2D version from https://arxiv.org/abs/1711.08506. |
diff --git a/source/code/_autosummary/napari_cellseg3d.code_models.models.wnet.model.html b/source/code/_autosummary/napari_cellseg3d.code_models.models.wnet.model.html
index 8b6961e6..a6bbb3f1 100644
--- a/source/code/_autosummary/napari_cellseg3d.code_models.models.wnet.model.html
+++ b/source/code/_autosummary/napari_cellseg3d.code_models.models.wnet.model.html
@@ -3,11 +3,11 @@
-
+
-
+
napari_cellseg3d.code_models.models.wnet.model — napari-cellseg3d Documentation
@@ -45,6 +45,7 @@
+
@@ -67,7 +68,7 @@
-
+
@@ -427,14 +428,10 @@ napari_cellseg3d.code_models.models.wnet.model
-napari_cellseg3d.code_models.models.wnet.model
+napari_cellseg3d.code_models.models.wnet.model
Implementation of a 3D W-Net model, based on the 2D version from https://arxiv.org/abs/1711.08506. The model performs unsupervised segmentation of 3D images.
Classes
-
-
-
-
Block (in_channels, out_channels[, dropout])
|
Basic block of the U-Net architecture. |
diff --git a/source/code/_autosummary/napari_cellseg3d.code_models.models.wnet.soft_Ncuts.html b/source/code/_autosummary/napari_cellseg3d.code_models.models.wnet.soft_Ncuts.html
index 87983fd3..cc192303 100644
--- a/source/code/_autosummary/napari_cellseg3d.code_models.models.wnet.soft_Ncuts.html
+++ b/source/code/_autosummary/napari_cellseg3d.code_models.models.wnet.soft_Ncuts.html
@@ -3,11 +3,11 @@
-
+
-
+
napari_cellseg3d.code_models.models.wnet.soft_Ncuts — napari-cellseg3d Documentation
@@ -45,6 +45,7 @@
+
@@ -67,7 +68,7 @@
-
+
@@ -427,16 +428,12 @@ napari_cellseg3d.code_models.models.wnet.soft_Ncuts
-napari_cellseg3d.code_models.models.wnet.soft_Ncuts
+napari_cellseg3d.code_models.models.wnet.soft_Ncuts
Implementation of a 3D Soft N-Cuts loss based on https://arxiv.org/abs/1711.08506 and https://ieeexplore.ieee.org/document/868688.
The implementation was adapted and approximated to reduce computational and memory cost.
This faster version was proposed on fkodom/wnet-unsupervised-image-segmentation.
Classes
-
-
-
-
SoftNCutsLoss (data_shape, device, ...[, radius])
|
Implementation of a 3D Soft N-Cuts loss based on https://arxiv.org/abs/1711.08506 and https://ieeexplore.ieee.org/document/868688. |
diff --git a/source/code/_autosummary/napari_cellseg3d.code_models.worker_inference.html b/source/code/_autosummary/napari_cellseg3d.code_models.worker_inference.html
index 1ab5baea..dc22d420 100644
--- a/source/code/_autosummary/napari_cellseg3d.code_models.worker_inference.html
+++ b/source/code/_autosummary/napari_cellseg3d.code_models.worker_inference.html
@@ -3,11 +3,11 @@
-
+
-
+
napari_cellseg3d.code_models.worker_inference — napari-cellseg3d Documentation
@@ -45,6 +45,7 @@
+
@@ -67,7 +68,7 @@
-
+
@@ -427,14 +428,10 @@ napari_cellseg3d.code_models.worker_inference
-napari_cellseg3d.code_models.worker_inference
+napari_cellseg3d.code_models.worker_inference
Contains the InferenceWorker class, which is a custom worker to run inference jobs in.
Module Attributes
-
-
-
-
EXPERIMENTAL_AUTO_DISCARD_EMPTY_REGIONS
|
Whether to automatically discard erroneously over-labeled empty regions from semantic segmentation or not. |
@@ -449,10 +446,6 @@ napari_cellseg3d.code_models.worker_inference
Classes
-
-
-
-
InferenceWorker (worker_config)
|
A custom worker to run inference jobs in. |
diff --git a/source/code/_autosummary/napari_cellseg3d.code_models.worker_training.html b/source/code/_autosummary/napari_cellseg3d.code_models.worker_training.html
index 63fb88bd..b4b327a3 100644
--- a/source/code/_autosummary/napari_cellseg3d.code_models.worker_training.html
+++ b/source/code/_autosummary/napari_cellseg3d.code_models.worker_training.html
@@ -3,11 +3,11 @@
-
+
-
+
napari_cellseg3d.code_models.worker_training — napari-cellseg3d Documentation
@@ -45,6 +45,7 @@
+
@@ -67,7 +68,7 @@
-
+
@@ -427,14 +428,10 @@ napari_cellseg3d.code_models.worker_training
-napari_cellseg3d.code_models.worker_training
+napari_cellseg3d.code_models.worker_training
Contains the workers used to train the models.
Classes
-
-
-
-
SupervisedTrainingWorker (worker_config)
|
A custom worker to run supervised training jobs in. |
diff --git a/source/code/_autosummary/napari_cellseg3d.code_models.workers_utils.html b/source/code/_autosummary/napari_cellseg3d.code_models.workers_utils.html
index 59537ae0..a90fd19d 100644
--- a/source/code/_autosummary/napari_cellseg3d.code_models.workers_utils.html
+++ b/source/code/_autosummary/napari_cellseg3d.code_models.workers_utils.html
@@ -3,11 +3,11 @@
-
+
-
+
napari_cellseg3d.code_models.workers_utils — napari-cellseg3d Documentation
@@ -45,6 +45,7 @@
+
@@ -67,7 +68,7 @@
-
+
@@ -427,14 +428,10 @@ napari_cellseg3d.code_models.workers_utils
-napari_cellseg3d.code_models.workers_utils
+napari_cellseg3d.code_models.workers_utils
Several worker-related utilities for inference and training.
Classes
-
-
-
-
InferenceResult ([image_id, original, ...])
|
Class to record results of a segmentation job. |
diff --git a/source/code/_autosummary/napari_cellseg3d.code_plugins.html b/source/code/_autosummary/napari_cellseg3d.code_plugins.html
index 83043bf3..c9731e7d 100644
--- a/source/code/_autosummary/napari_cellseg3d.code_plugins.html
+++ b/source/code/_autosummary/napari_cellseg3d.code_plugins.html
@@ -3,11 +3,11 @@
-
+
-
+
napari_cellseg3d.code_plugins — napari-cellseg3d Documentation
@@ -45,6 +45,7 @@
+
@@ -67,7 +68,7 @@
-
+
@@ -427,14 +428,10 @@ napari_cellseg3d.code_plugins
-napari_cellseg3d.code_plugins
+napari_cellseg3d.code_plugins
This folder contains all plugin-related code.
Modules
-
-
-
-
napari_cellseg3d.code_plugins.plugin_base
|
Base classes for napari_cellseg3d plugins. |
diff --git a/source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_base.html b/source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_base.html
index a366f1db..08b039f5 100644
--- a/source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_base.html
+++ b/source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_base.html
@@ -3,11 +3,11 @@
-
+
-
+
napari_cellseg3d.code_plugins.plugin_base — napari-cellseg3d Documentation
@@ -45,6 +45,7 @@
+
@@ -67,7 +68,7 @@
-
+
@@ -427,14 +428,10 @@ napari_cellseg3d.code_plugins.plugin_base
-napari_cellseg3d.code_plugins.plugin_base
+napari_cellseg3d.code_plugins.plugin_base
Base classes for napari_cellseg3d plugins.
Classes
-
-
-
-
BasePluginFolder (viewer[, parent, ...])
|
A basic plugin template for working with folders of images. |
diff --git a/source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_convert.html b/source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_convert.html
index acc33ac0..51488778 100644
--- a/source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_convert.html
+++ b/source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_convert.html
@@ -3,11 +3,11 @@
-
+
-
+
napari_cellseg3d.code_plugins.plugin_convert — napari-cellseg3d Documentation
@@ -45,6 +45,7 @@
+
@@ -67,7 +68,7 @@
-
+
@@ -427,14 +428,10 @@ napari_cellseg3d.code_plugins.plugin_convert
-napari_cellseg3d.code_plugins.plugin_convert
+napari_cellseg3d.code_plugins.plugin_convert
Several image processing utilities.
Classes
-
-
-
-
AnisoUtils (viewer[, parent])
|
Class to correct anisotropy in images. |
diff --git a/source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_crf.html b/source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_crf.html
index 97e44fdc..44d4593a 100644
--- a/source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_crf.html
+++ b/source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_crf.html
@@ -3,11 +3,11 @@
-
+
-
+
napari_cellseg3d.code_plugins.plugin_crf — napari-cellseg3d Documentation
@@ -45,6 +45,7 @@
+
@@ -67,7 +68,7 @@
-
+
@@ -427,14 +428,10 @@ napari_cellseg3d.code_plugins.plugin_crf
-napari_cellseg3d.code_plugins.plugin_crf
+napari_cellseg3d.code_plugins.plugin_crf
CRF plugin for napari_cellseg3d.
Classes
-
-
-
-
CRFParamsWidget ([parent])
|
Use this widget when adding the crf as part of another widget (rather than a standalone widget). |
diff --git a/source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_crop.html b/source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_crop.html
index 041c6e7c..e2fd196a 100644
--- a/source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_crop.html
+++ b/source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_crop.html
@@ -3,11 +3,11 @@
-
+
-
+
napari_cellseg3d.code_plugins.plugin_crop — napari-cellseg3d Documentation
@@ -45,6 +45,7 @@
+
@@ -67,7 +68,7 @@
-
+
@@ -427,14 +428,10 @@ napari_cellseg3d.code_plugins.plugin_crop
-napari_cellseg3d.code_plugins.plugin_crop
+napari_cellseg3d.code_plugins.plugin_crop
Crop utility plugin for napari_cellseg3d.
Classes
-
-
-
-
Cropping (viewer[, parent])
|
A utility plugin for cropping 3D volumes. |
diff --git a/source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_helper.html b/source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_helper.html
index 0e1b0ae7..60a9a9f1 100644
--- a/source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_helper.html
+++ b/source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_helper.html
@@ -3,11 +3,11 @@
-
+
-
+
napari_cellseg3d.code_plugins.plugin_helper — napari-cellseg3d Documentation
@@ -45,6 +45,7 @@
+
@@ -67,7 +68,7 @@
-
+
@@ -427,14 +428,10 @@ napari_cellseg3d.code_plugins.plugin_helper
-napari_cellseg3d.code_plugins.plugin_helper
+napari_cellseg3d.code_plugins.plugin_helper
Tiny plugin showing link to documentation and about page.
Classes
-
-
-
-
Helper (*args, **kwargs)
|
Tiny plugin showing link to documentation and about page. |
diff --git a/source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_metrics.html b/source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_metrics.html
index 49d9c97d..f3958792 100644
--- a/source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_metrics.html
+++ b/source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_metrics.html
@@ -3,11 +3,11 @@
-
+
-
+
napari_cellseg3d.code_plugins.plugin_metrics — napari-cellseg3d Documentation
@@ -45,6 +45,7 @@
+
@@ -67,7 +68,7 @@
-
+
@@ -427,14 +428,10 @@ napari_cellseg3d.code_plugins.plugin_metrics
-napari_cellseg3d.code_plugins.plugin_metrics
+napari_cellseg3d.code_plugins.plugin_metrics
CURRENTLY UNUSED.
Classes
-
-
-
-
MetricsUtils (viewer[, parent])
|
Plugin to evaluate metrics between two sets of labels, ground truth and prediction. |
diff --git a/source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_model_inference.html b/source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_model_inference.html
index 0f621512..09fb200d 100644
--- a/source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_model_inference.html
+++ b/source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_model_inference.html
@@ -3,11 +3,11 @@
-
+
-
+
napari_cellseg3d.code_plugins.plugin_model_inference — napari-cellseg3d Documentation
@@ -45,6 +45,7 @@
+
@@ -67,7 +68,7 @@
-
+
@@ -427,14 +428,10 @@ napari_cellseg3d.code_plugins.plugin_model_inference
-napari_cellseg3d.code_plugins.plugin_model_inference
+napari_cellseg3d.code_plugins.plugin_model_inference
Inference plugin for napari_cellseg3d.
Classes
-
-
-
-
Inferer (*args, **kwargs)
|
A plugin to run already trained models in evaluation mode to preform inference and output a label on all given volumes. |
diff --git a/source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_model_training.html b/source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_model_training.html
index 78e50356..8f82d9e0 100644
--- a/source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_model_training.html
+++ b/source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_model_training.html
@@ -3,11 +3,11 @@
-
+
-
+
napari_cellseg3d.code_plugins.plugin_model_training — napari-cellseg3d Documentation
@@ -45,6 +45,7 @@
+
@@ -67,7 +68,7 @@
-
+
@@ -427,14 +428,10 @@ napari_cellseg3d.code_plugins.plugin_model_training
-napari_cellseg3d.code_plugins.plugin_model_training
+napari_cellseg3d.code_plugins.plugin_model_training
Training plugin for napari_cellseg3d.
Classes
-
-
-
-
LearningRateWidget ([parent])
|
A widget to choose the learning rate. |
diff --git a/source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_review.html b/source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_review.html
index 81937ea3..2532a6a4 100644
--- a/source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_review.html
+++ b/source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_review.html
@@ -3,11 +3,11 @@
-
+
-
+
napari_cellseg3d.code_plugins.plugin_review — napari-cellseg3d Documentation
@@ -45,6 +45,7 @@
+
@@ -67,7 +68,7 @@
-
+
@@ -427,14 +428,10 @@ napari_cellseg3d.code_plugins.plugin_review
-napari_cellseg3d.code_plugins.plugin_review
+napari_cellseg3d.code_plugins.plugin_review
Review plugin for 3D labeling of volumes.
Classes
-
-
-
-
Reviewer (*args, **kwargs)
|
A plugin for selecting volumes and labels file and launching the review process. |
diff --git a/source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_review_dock.html b/source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_review_dock.html
index f0478c19..5abaacb5 100644
--- a/source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_review_dock.html
+++ b/source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_review_dock.html
@@ -3,11 +3,11 @@
-
+
-
+
napari_cellseg3d.code_plugins.plugin_review_dock — napari-cellseg3d Documentation
@@ -45,6 +45,7 @@
+
@@ -67,7 +68,7 @@
-
+
@@ -427,14 +428,20 @@ napari_cellseg3d.code_plugins.plugin_review_dock
-napari_cellseg3d.code_plugins.plugin_review_dock
+napari_cellseg3d.code_plugins.plugin_review_dock
Widget opened when a new Review session is started.
+Module Attributes
+
+
+logger
|
+plugin_dock.py
+
+Definition of Datamanager widget, for saving labels status in csv file |
+
+
+
Classes
-
-
-
-
Datamanager (parent)
|
A widget with a single checkbox that allows to store the status of a slice in csv file (checked/not checked). |
diff --git a/source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_utilities.html b/source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_utilities.html
index d13c7e1b..893a2412 100644
--- a/source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_utilities.html
+++ b/source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_utilities.html
@@ -3,11 +3,11 @@
-
+
-
+
napari_cellseg3d.code_plugins.plugin_utilities — napari-cellseg3d Documentation
@@ -45,6 +45,7 @@
+
@@ -67,7 +68,7 @@
-
+
@@ -427,14 +428,10 @@ napari_cellseg3d.code_plugins.plugin_utilities
-napari_cellseg3d.code_plugins.plugin_utilities
+napari_cellseg3d.code_plugins.plugin_utilities
Central plugin for all utilities.
Classes
-
-
-
-
Utilities (*args, **kwargs)
|
Central plugin for all utilities. |
diff --git a/source/code/_autosummary/napari_cellseg3d.interface.html b/source/code/_autosummary/napari_cellseg3d.interface.html
index 43d02a41..dd8720bc 100644
--- a/source/code/_autosummary/napari_cellseg3d.interface.html
+++ b/source/code/_autosummary/napari_cellseg3d.interface.html
@@ -3,11 +3,11 @@
-
+
-
+
napari_cellseg3d.interface — napari-cellseg3d Documentation
@@ -45,6 +45,7 @@
+
@@ -67,7 +68,7 @@
-
+
@@ -427,14 +428,36 @@ napari_cellseg3d.interface
-napari_cellseg3d.interface
+napari_cellseg3d.interface
User interface functions and aliases.
+Module Attributes
+
+
+LEFT_AL
|
+Alias for Qt.AlignmentFlag.AlignLeft, to use in addWidget |
+
+RIGHT_AL
|
+Alias for Qt.AlignmentFlag.AlignRight, to use in addWidget |
+
+HCENTER_AL
|
+Alias for Qt.AlignmentFlag.AlignHCenter, to use in addWidget |
+
+CENTER_AL
|
+Alias for Qt.AlignmentFlag.AlignCenter, to use in addWidget |
+
+ABS_AL
|
+Alias for Qt.AlignmentFlag.AlignAbsolute, to use in addWidget |
+
+BOTT_AL
|
+Alias for Qt.AlignmentFlag.AlignBottom, to use in addWidget |
+
+TOP_AL
|
+Alias for Qt.AlignmentFlag.AlignTop, to use in addWidget |
+
+
+
Functions
-
-
-
-
add_blank (widget[, layout])
|
Adds a space between consecutive buttons/labels in a layout when building a widget. |
@@ -482,10 +505,6 @@ napari_cellseg3d.interface
Classes
-
-
-
-
AnisotropyWidgets ([parent, default_x, ...])
|
Class that creates widgets for anisotropy handling. |
diff --git a/source/code/_autosummary/napari_cellseg3d.utils.html b/source/code/_autosummary/napari_cellseg3d.utils.html
index 1ccaff1d..650b137a 100644
--- a/source/code/_autosummary/napari_cellseg3d.utils.html
+++ b/source/code/_autosummary/napari_cellseg3d.utils.html
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napari_cellseg3d.utils — napari-cellseg3d Documentation
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Utilities functions, classes, and variables.
Functions
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align_array_sizes (array_shape, target_shape)
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Aligns the sizes of two arrays by adding zeros to the smaller one. |
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Classes
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Singleton
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Singleton class that can only be instantiated once at a time, with said unique instance always being accessed on call. |
diff --git a/source/code/api.html b/source/code/api.html
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API reference — napari-cellseg3d Documentation
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napari_cellseg3d.interface
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User interface functions and aliases. |
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Cropping✂️ — napari-cellseg3d Documentation
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