| ... | ... | @@ -26,7 +26,8 @@ This is a function, which in most cases does affect the final segmentation and p |
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**6.) Filter particles by size:**
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With thee
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The particles to detect can be filtered by their size for excluding too small particles. The function "measure fraction of particles" is currently still included for testing or demonstration purposes only. When set to any value smaller than 1.0, only a random fraction of the particles will be considered, according to the value (e.g. 0.3 means that 30 % of the particles is used). *Important Note:* The algorithm does not exactly give 30 % when set to 0.3, but approaches the value if the number of particles is sufficiently high. Do not take it for aliquotation of the sample. If you absolutely have to, run the particle detection once with fraction set to 1.0, note the total particle number and then run again with a lower fraction value. Note the new number and calculate the exact measured fraction!
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**7.) Show sure foreground:**
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This preview shows how the "sure foreground", which is the starting point for the actual watershed algorithm, looks like. Everything in green will be definitely a particle, whereas each yellow spot depicts the center of each individual particle.
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| ... | ... | @@ -36,6 +37,12 @@ This preview shows how the "sure foreground", which is the starting point for th |
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Starting from the previously shown yellow dots the watershed algorithm tries to find particle borders. This can be controlled to some extent using the "compactness", a float value ranging from 0 to 1. It effects how "straight" the borders will be. The below image shows the two extremes of 0 (curvy boundaries) to 1 (perfectly straight boundaries). In most cases, values between 0 and 0.1 are useful. Clicking on **"show matershed markers"** displays the currently produced boarders.
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**9.)
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**9.) Detect, Detect all, Clear detection:**
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Clicking on "detect" applies the parameters to the current preview, showing the final particle boarders and the measurement spots (refer to first overview image). Clicking on "detect all" applies the parameter to the entire fullimage, which can take a few minutes. "Clear detection" obviously deletes the currently detected particles.
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**10.) Manually editing the particles:**
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The algorithm is likely to fail at several cases in the fullimage, which makes it adequate to manually edit the detected particles. This can be done at any time in the preview window in the following ways:
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* a) Add seed points
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