Merge pull request #7 from pelkmanslab/cellprofiler_segmentation

Adding modules for segmentation as performed in cell profiler

jtlibrary/python/jtmodules/src/jtmodules/segment_secondary_cp.handles.yaml

@@ -0,0 +1,81 @@
+---
+version: 0.0.1
+
+input:
+
+  - name: primary_label_image
+    type: LabelImage
+    key:
+    help: >
+      Labeled image encoding primary objects that should be used as seeds for
+      the detection of secondary objects.
+
+  - name: intensity_image
+    type: IntensityImage
+    key:
+    help: >
+      Grayscale image that should be used to find the outlines of secondary
+      objects.
+
+  - name: threshold
+    type: Numeric
+    value: 125
+    help: >
+      Maximum value of background.
+
+  - name: method
+    type: Scalar
+    value: propagation
+    options:
+      - propagation
+      - watershed_gradient
+      - watershed_image
+      - distance_n
+      - distance_b
+    help: >
+      Segmentation method.
+
+  - name: regularization_factor
+    type: Numeric
+    value: 0.01
+    help: >
+      Used only for 'propagation' method. Larger values cause the distance
+      between objects to be more important than the intensity image in
+      determining cut lines. Smaller values cause the intensity image to
+      be more important than the distance between objects.
+
+  - name: distance_to_dilate
+    type: Numeric
+    value: 3
+    help: >
+      Used only for 'distance_n', 'distance_b' methods. The number of
+      pixels by which the primary objects will be expanded.
+
+  - name: fill_holes
+    type: Boolean
+    value: true
+    help: Should holes in the secondary objects be filled?
+
+  - name: plot
+    type: Plot
+    value: false
+    help: Should a figure be created?
+
+output:
+
+  - name: secondary_label_image
+    type: LabelImage
+    key: segment_secondary.secondary_label_image
+    help: Labeled image encoding secondary objects.
+
+  - name: figure
+    type: Figure
+    help: >
+      Comparison of "primary_label_image" and "secondary_label_image". Also
+      shows outlines of objects in "secondary_label_image" on "intensity_image".
+
+
+
+
+
+