deploy: e00806c

Author: C-Achard

.doctrees/environment.pickle

@@ -1,6 +1,29 @@
 model_instance_seg.py
 ===========================================
 
+Classes
+-------------
+
+InstanceMethod
+**************************************
+.. autoclass:: napari_cellseg3d.code_models.model_instance_seg::InstanceMethod
+    :members: __init__
+
+ConnectedComponents
+**************************************
+.. autoclass:: napari_cellseg3d.code_models.model_instance_seg::ConnectedComponents
+    :members: __init__
+
+Watershed
+**************************************
+.. autoclass:: napari_cellseg3d.code_models.model_instance_seg::Watershed
+    :members: __init__
+
+VoronoiOtsu
+**************************************
+.. autoclass:: napari_cellseg3d.code_models.model_instance_seg::VoronoiOtsu
+    :members: __init__
+
 
 Functions
 -------------

.doctrees/res/code/model_instance_seg.doctree

@@ -19,11 +19,6 @@ ToSemanticUtils
 .. autoclass:: napari_cellseg3d.code_plugins.plugin_convert::ToSemanticUtils
     :members: __init__
 
-InstanceWidgets
-**********************************
-.. autoclass:: napari_cellseg3d.code_plugins.plugin_convert::InstanceWidgets
-    :members: __init__, run_method
-
 ToInstanceUtils
 **********************************
 .. autoclass:: napari_cellseg3d.code_plugins.plugin_convert::ToInstanceUtils

.doctrees/res/code/plugin_convert.doctree

@@ -33,9 +33,9 @@ If you'd like to change the size of the volume, change the parameters as previou
 
 Creating new layers
 ---------------------------------
-To "zoom in" your volume, you can use the "Create new layers" checkbox to make a new layer not controlled by the plugin next
-time you hit Start. This way, you can first select your region of interest by using the tool as described above,
-the enable the option, select the cropped layer, and define a smaller crop size to have easier access to your region of interest.
+To "zoom in" your volume, you can use the "Create new layers" checkbox to make a new cropping layer controlled by the sliders
+next time you hit Start. This way, you can first select your region of interest by using the tool as described above,
+then enable the option, select the cropped region produced before as the input layer, and define a smaller crop size in order to crop within your region of interest.
 
 Interface & functionalities
 ---------------------------------------------------------------

.doctrees/res/guides/cropping_module_guide.doctree

@@ -4,13 +4,21 @@ Label conversion utility guide
 ==================================
 
 This utility will let you convert labels to various different formats.
+
 You will have to specify the results directory for saving; afterwards you can run each action on a folder or on the currently selected layer.
 
 You can :
 
+* Crop 3D volumes :
+    Please refer to :ref:`cropping_module_guide` for a guide on using the cropping utility.
+
 * Convert to instance labels :
-    This will convert 0/1 semantic labels to instance label, with a unique ID for each object using the watershed method.
+    This will convert 0/1 semantic labels to instance label, with a unique ID for each object.
+    The available methods for this are :
 
+    * Connected components : simple method that will assign a unique ID to each connected component. Does not work well for touching objects (objects will often be fused), works for anisotropic volumes.
+    * Watershed : method based on topographic maps. Works well for touching objects and anisotropic volumes; touching objects may be fused.
+    * Voronoi-Otsu : method based on Voronoi diagrams. Works well for touching objects but only for isotropic volumes.
 * Convert to semantic labels :
     This will convert instance labels with unique IDs per object into 0/1 semantic labels, for example for training.