2.4 Cell Processing
- Microscope: select type of image acquisition (epi or SIM); used for cell cycle classification
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Classify Cell Cycle Phase: eHooke will automatically assign a cell cycle phase
- Currently works for Staphylococcus aureus. Can be used without DNA labelling, however accuracy decreases
- Membrane thickness: use 4 for epifluorescence images, 6 for SIM
- Find septum: eHooke will define the septum as the brightest region inside the cell
- Find open septum: same as above but finds the two brightest regions and consider both as a septum, in order to detect open septa
- Look for septum in base: uses base channel instead of fluorescence to define septum
- Look for septum in secondary: uses secondary channel instead of fluorescence to define septum
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Septum algorithm:
- Isodata: based on fluorescence
- Box: based on center axis (shouldn’t be used)
Manual: right-click on a cell to select/unselect
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Automatic: based on filters, optional image signal, select based on a previous report and cell cycle classification. Automatic selection is additive meaning will add newly selected cells to previous selection.
- Use Select All, Reject All and Invert Selection accordingly