usage:segmentation

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usage:segmentation [2022/09/05 23:04] – pseudomoanerusage:segmentation [2022/10/20 10:35] (current) – pseudomoaner
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 To run this module, click the **Segmentation** button on the home panel. This should bring up the following GUI: To run this module, click the **Segmentation** button on the home panel. This should bring up the following GUI:
  
-{{ :usage:segmentationannotated.png?800 |}}+{{ :usage:segmentationannotatednew.png?800 |}}
  
 To begin, you will need to set the channel you wish to use for segmentation using the **segmentation channel** dropdown menu. Channel 1 is typically the brightfield/phase channel, with additional channels associated fluorescence images. You will also need to choose if the objects within this image are bright or dark relative to the background. The appropriate option should be selected in the **Foreground colour** field. To begin, you will need to set the channel you wish to use for segmentation using the **segmentation channel** dropdown menu. Channel 1 is typically the brightfield/phase channel, with additional channels associated fluorescence images. You will also need to choose if the objects within this image are bright or dark relative to the background. The appropriate option should be selected in the **Foreground colour** field.
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 In the first stage of the pipeline, a texture metric is applied to the image. This provides a general separation of foreground (textured regions) and background (untextured regions), without necessarily separating closely-packed objects. In this overlay, red indicates regions classified as forground (objects): In the first stage of the pipeline, a texture metric is applied to the image. This provides a general separation of foreground (textured regions) and background (untextured regions), without necessarily separating closely-packed objects. In this overlay, red indicates regions classified as forground (objects):
  
-{{ :usage:segmentationthresh.png?800 |}}+{{ :usage:segmentationthreshnew.png?800 |}}
  
 The texture analysis stage is associated with two parameters: The texture analysis stage is associated with two parameters:
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 In this overlay, red regions indicate the binary ridges that are subtracted from the binary texture image to generate an initial segmentation: In this overlay, red regions indicate the binary ridges that are subtracted from the binary texture image to generate an initial segmentation:
  
-{{ :usage:segmentationridge.png?800 |}}+{{ :usage:segmentationridgenew.png?800 |}}
  
 This initial segmentation is next refined by the application of the watershed algorithm. This initial segmentation is next refined by the application of the watershed algorithm.
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 Choosing next the **Watershed** overlay option, your view should now switch to one consisting of red and yellow outlines: Choosing next the **Watershed** overlay option, your view should now switch to one consisting of red and yellow outlines:
  
-{{ :usage:segmentationwatershed.png?800 |}}+{{ :usage:segmentationwatershednew.png?800 |}}
  
 These indicate the segmentation boundaries set by the combination of the threshold and ridge detection stages (yellow), and the boundaries added by the morphological watershed stage (red). These indicate the segmentation boundaries set by the combination of the threshold and ridge detection stages (yellow), and the boundaries added by the morphological watershed stage (red).
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 When the **Segmentation** overlay is chosen, you will be able to vary the **Object area threshold (low)** and **Object area threshold (high)** parameters. These parameters set the minimum and maximum area (in pixels) an object is allowed to fall between to be included in the final segmentation. In this overlay, each segmented object is indicated by a separate colour: When the **Segmentation** overlay is chosen, you will be able to vary the **Object area threshold (low)** and **Object area threshold (high)** parameters. These parameters set the minimum and maximum area (in pixels) an object is allowed to fall between to be included in the final segmentation. In this overlay, each segmented object is indicated by a separate colour:
  
-{{ :usage:segmentationfinal.png?800 |}}+{{ :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> 
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 +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> 
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 +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. 
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 +</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.  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. 
  • usage/segmentation.txt
  • Last modified: 2022/10/20 10:35
  • by pseudomoaner