Feature Based
Mark local maxima
This step will find local maxima of a chosen label and mark these with another chosen label.
| Option | Description |
|---|---|
| Label | Choose a label in which to search for local maxima. |
| Mark with | Choose the label to use for marking the local maxima. |
| Feature | Choose which feature image the local maxima should be found in. |
| Threshold | Select a threshold for intensity values not supposed to be included in the analysis. If for instance a value of 200 is set, the algorithm will not place any local maxima for value below 200 even though they fulfill the criteria for a local maximum. |
Mark max intensity areas
This step will find max intensity areas (maxima areas) of a chosen feature e.g. an object heatmap and mark these with a ROI. The different parameters should be specified:
| Option | Description |
|---|---|
| Input feature | Choose a feature in which to search for max intensity areas. |
| Marking ROI | Choose which ROI (e.g. Default) that is used to mark max intensity areas. |
| Method | Choose the method on how to detect maxima areas: |
| Square - Use a simple square to mark maxima areas. | |
| Circle - Use a simple circle to mark maxima areas. The circular hot spot corresponds to looking through a microscope, and thus most closely matches current guidelines for hot spot estimation. When working with a circular hot spot, the drawing radius of the heatmap should correspond to the radius of the hot spot to ensure that the cells contributing to a high value in the heatmap are counted in the found hot spot. | |
| Hotspot Area - Mark maxima areas with a ROI area that follows the intensity of the feature. Technically, a ROI is drawn by selecting a max intensity region (pixel) and then grow the ROI in the direction of decreasing intensity until the Total size is reached. There is also an option to select Min ROI size. This means that if an ROI marks a maxima but the area of that ROI is below the Min ROI size, it will increase by following the intensity until the area is at least the Min ROI size. In general, when using the heatmap shaped hot spots, a smaller drawing radius should be used for heatmap. This is to avoid having cells from far away contribute to hot spots, and then not be included in the found hot spot because they were outside the hottest contours of the heatmap. | |
| Hotspot Count - Mark maxima areas based on the count/number of certain object labels, e.g. classified nuclei. | |
| Total size | Enter the total size of all maxima for Hotspot Area or enter the total number of objects inside all maxima for Hotspot Count. |
| Number of ROI's | Enter the maximum number of maxima areas that can be marked. |
| Min Center Dist | Enter the minimum distance that determines how close two local maxima can be. The minimum distance is from the center of each area. Only applies for Circle and Square. |
| Min ROI size | Minimum size of the individual maxima areas using Hotspot Area or minimum number of object in the maxima areas using Hotspot Count. |
| Objects | The label object which should be used for Hotspot Count e.g. number of nuclei ("Label001"). |