Full Detection with Mask Processor

If you want to analyze all events in a sample but do not want to segment each fluorescent channel separately but want to copy the segmentation from one channel to another one you can use the Full Detection with Mask processor. After you pressed "Process" a window will open where you have to specify for every fluorescent channel which channel you want to copy the segmentation from.

With the plus and minus sign you can adjust the number of channels you have in your sample, the first line always remains as shown. In the second line (in the screenshot filled with 2 2 3 3) you can now specify the segmentation mask you want to use. If you fill in 1,2,3,4 (so first and second lineage the same) this processor does exactly the same as the Full Detection processor. In the example shown, the signal in channel 1 and 4 are not segment but the mask of channel 2 is used also in channel 1 and the mask of channel 3 is used also for channel 4. Note that for each channel you have to select if you want to dilate the mask or not. If you tick that checkbox the mask from the specified channel is copied but inflated by a few pixels. This is helpful, if you expect that the fluorescent signal in the channel you want to copy the segmentation mask from is smaller than the signal in the target channel. An example is that you want to segment in the fluorescent channel highlighting the nucleus but want to copy the mask to another channel where you expect the fluorescent signal to surround the nucleus signal.

This processor can be helpful in cases where you want to segment only single channels (fill in a 0 in all channels that you want to exclude from further analysis) or if a signal is very dim in your target channel or you saw difficulties in the segmentation but you still want to evaluate the channel.