You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Copy file name to clipboardExpand all lines: docs/res/guides/detailed_walkthrough.rst
+8-5Lines changed: 8 additions & 5 deletions
Display the source diff
Display the rich diff
Original file line number
Diff line number
Diff line change
@@ -3,7 +3,7 @@
3
3
Detailed walkthrough
4
4
===================================
5
5
6
-
The following guide will show in details how to use the plugin's workflow, starting from a large labeled volume.
6
+
The following guide will show you how to use the plugin's workflow, starting from human-labeled annotation volume, to running inference on novel volumes.
7
7
8
8
Preparing images and labels
9
9
-------------------------------
@@ -116,11 +116,14 @@ In most cases this should left enabled.
116
116
117
117
Finally, the last tab lets you choose :
118
118
119
-
* The model
119
+
* The models
120
120
121
-
* SegResNet is a lightweight model (low memory requirements) with decent performance.
122
-
* TRAILMAP is a recent model trained for axonal detection in cleared tissue; use it if your dataset is similar
123
-
* VNet is a possibly more performant model than SegResnet but requires much more memory
121
+
* SegResNet is a lightweight model (low memory requirements) from MONAI originally designed for 3D fMRI data.
122
+
* VNet is a heavier (than SegResNet) CNN from MONAI designed for medical image segmentation.
123
+
* TRAILMAP is our PyTorch implementation of a 3D CNN model trained for axonal detection in cleared tissue.
124
+
* TRAILMAP-MS is our implementation in PyTorch additionally trained on mouse cortical neural nuclei from mesoSPIM data.
125
+
* Note, the code is very modular, so it is relatively straightforward to use (and contribute) your model as well.
126
+
124
127
125
128
* The loss : for object detection in 3D volumes you'll likely want to use the Dice or Dice-focal Loss.
0 commit comments