Differences

This shows you the differences between two versions of the page.

--- usage:segmentation [2021/10/26 20:47] – pseudomoaner
+++ usage:segmentation [2022/10/20 10:35] (current) – pseudomoaner
@@ Line 70: / Line 70: @@
 {{ :usage:segmentationfinalnew.png?800 |}}
+The two segmentation refinement checkboxes provide additional tools to further improve the quality of your segmentation:
+  * **Remove halos**: This checkbox is intended for use with objects that are surrounded by bright halos, particularly phase-contrast images. The texture detection stage can struggle to separate these halos from the cell bodies, resulting in unwanted chunks of halo being detected as objects in the final segmentation. Upon selection of this option, the system will measure the average intensity of each segmented object and discard any that are substantially lighter than the dark population of objects.
+<note warning>
+If some frames of your dataset do not contain two distinct populations of segmented objects, this option will erroneously discard some of your target objects. If in doubt, leave the remove halos box unchecked.
+</note>
+{{ :usage:remhalosdemo.png?800 |}}
+  * **Recursive watershed**: If the set of segmentation stages up to this point fails to separate some objects, they will typically remain in the image as large, fused clumps. By default, these clumps are removed when the **Object Area Threshold (High)** slider is set to a value smaller than their area. However, an alternative approach is to attempt to resegment these objects using less stringent parameters. By checking this box, you can recursively apply the watershed segmentation stage, progressively reducing the watershed threshold until all sub-objects are smaller than the specified threshold.
+<note>
+The recursive watershed algorithm will terminate if the watershed threshold falls too low, and any remaining objects larger than the specified upper area threshold will be discarded.
+</note>
+{{ :usage:recurswaterdemo.png?800 |}}
 Once you are happy with your final segmentation, press the button labelled **Process 'em all** to start segmentation of the entire dataset. This will generate a new directory in your root directory and fill it with the segmented images.