Segmenting bacteria

 

 

When segmenting small objects, e.g. bacteria or fungal spores, Spots don't always work well. E.g, the fungi may vary in size too much, so no singular spot size will fit. Or, the cell wall may be sharply labelled, whilst the inner parts of the cells are not, in which case the Spots finder will fail (it will just place Spots on the bright periphery). In such cases, you can try the following:

1. Segment the small objects as Surfaces. Do you best to separate the individual objects, but also make sure that you segment everything you need. Do not worry too much about merged objects, we will separate them later.
2. Set up a Cells object on the same channel, but use the now-existing Surfaces representation of the small objects as input ("Imported from Surfaces = true"). Choose the Cell mode where there are only cell membrane labels provided´("Cell Type = Cell Body", see image below; i.e., no nuclei, no intracellular vesicles).    Set the Cells size accordingly, and let it segment. The results will be surprisingly good, nicely separating the objects that were merged in the Surfaces representation.

 

Segmented yeast as Cells:

 

 

Segmented yeast as Surfaces: