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Getting started with MaMuT

3 bytes removed, 06:30, 14 March 2017
Semi-automated tracking in MaMuT.
The semi-automatic tracking starts from a single cell in the selection. It inspects a neighborhood centered on this cell, but in the next time-point. The neighborhood is filtered by a Laplacian-of-Gaussian filter, tuned with the initial cell radius, and candidate cells are generated from the maxima in the filtered image. The filtered pixel-value of these maxima are used as a quality measure for candidate cell. The quality value is higher if the cell in the raw image is bright, and of radius similar to that of the initial cell.
Amongst these candidates, only those who have a quality higher than a fraction of the initial cell are retained. You set this parameter using the <tt style="font-size: 1.25em;">Quality threshold</tt> parameter in the \textbf{'''Semi-automatic tracking panel}'''. Only candidates with a quality larger than the quality of the initial cell times this threshold will be retained. Cells that are placed manually do not have a quality value (it shows up as -1 if you query it), so all the candidates cells are automatically accepted.
Candidates are then filtered by distance to the initial cell. Candidates that are found further away than <tt style="font-size: 1.25em;">Distance tolerance</tt> times the initial cell radius are discarded.
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