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The topic of this +thesis is the expansion of this software with a new watershed workflow. +The workflow needs to be able to handle the following use cases where the following data +can be supplied: +1.) seeds (nuclei) and/or 2.) boundaries + +• Seeded Watershed: +1. only seeds: pointless to do a seeded watershed with seeds only. +2. boundaries and seeds: use a seeded watershed on boundaries with the supplied seeds. The seeds can be changed, removed or new seeds can be drawn manually. +3. only boundaries: generate seeds out of the boundaries and label them. Carry +out the use case where the seeds and the boundaries are supplied. + +• Unseeded Watershed should still be possible when only using the boundaries. + +In ilastik a workflow is made up of several applets that are connected with each other. +The seeds applet contains the functionality of generating seeds and sets the watershed +algorithm to seeded or unseeded. It is possible to manipulate, create or delete seeds +manually in the watershed applet. The watersheds of the boundaries with the given seeds +can be computed and visualized. Any change to the seeds and their impacts on the +watersheds are visible immediately. In the end the resulting data can be exported. +" **cited from [chapter 1. Introduction] Andreas Haller, Master Thesis, "Interactive Watershed Based Segmentation For Biological Images", March 2017, Heidelberg University** + + + +## Generate Seeds +"In the seeds applet the user can view all provided inputs, generate new seeds constructing +them on the given boundaries or decide whether the following watershed should be carried +out unseeded independently of given/generated seeds. + +**Usage** + +• Unseeded: +if checked, the watershed algorithm will be an unseeded Union Find algorithm + +• Smoothing: +a selection of smoothing methods can be chosen + +• Sigma: +the smoothing parameter that describes the intensity of smoothing + +• Compute Method: +a selection of methods that can be chosen to compute the generated seeds + +• Generate Seeds Button: +needs to be clicked to generate seeds and override any provided seeds with generated +ones + +Seeds are generated by: +1. smoothing the boundaries with the given smoothing method and the given sigma +2. computing seeds on the basis of the smoothed image with the selected compute +method + + +" **cited from [chapter 3.2.2 Seeds Applet] Andreas Haller, Master Thesis, "Interactive Watershed Based Segmentation For Biological Images", March 2017, Heidelberg University** + +If the image of the supplied seeds is binary, this image is automatically labeled where 0 is background. + + +## Interactive Watershed Segmentation with manipulation of Seeds + +"In the watershed applet the user can execute a watershed algorithm. This algorithm +depends on the watershed method that is passed on by the seeds applet. Additionally, +the user can manually modify, delete and create new seeds. It is possible to reset any +changes to the supplied seeds. The impact of these changes on the results of the watershed +algorithm can be directly seen. + +• Neighbors: +specify the number of pixel that are taken into account +* direct: 2D means 4 neighbors & + 3D means 8 neighbors +* indirect: 2D means 6 neighbors & + 3D means 26 neighbors + +• Show “Corrected Seeds” pixel value: +shows the pixel value of the “Corrected Seeds” layer where the cursor points to + +• Reset “Corrected Seeds” to “Seeds”: +remove all changes on the seeds that are done manually (that are displayed in the +“Corrected Seeds” layer), so that they are identical to the “Seeds” layer, which +displays the originally input seeds + +• Drawing/deleting/changing labels: +– drawing: +select a given seed, click on the brush icon and draw into the image +– deleting: +click on the red circle with a cross inside to delete the label from the label list +and its associated pixels from the ”Corrected Seeds“ image +– clearing: +right click on a label and click ”clear Label“ to remove all pixels with this value +from the seeds image. This label isn’t removed from the label list and can be +used later on +– ”Add Seed“ button: +add an additional label (limit: 254 labels) +– rubber: +reset everything under the cursor to 0 + +• run seeded watershed: +execute the watershed algorithm on the boundaries. If seeded, then use the ”Corrected Seeds“ as seeds + + + +" **cited from [chapter 3.2.3 Watershed Applet] Andreas Haller, Master Thesis, "Interactive Watershed Based Segmentation For Biological Images", March 2017, Heidelberg University** +