Cell Type Optimization

For many cell types, the default cell type values provided in the software are suitable. For some Cell
Lines, parameters will need to be changed to optimize the analysis of the cells.

 

 

Cell Type Parameters

Typical Range

Full Range

Increase Value

Decrease Value

When/Why You Would Want to Change This

Warnings

Defines whether there is a cell present or not

Minimum Diameter

5 to 12 µm

1 to 60 µm

Less cells identified

More cells identified

Software is excluding small cells (circled blue)

Debris included in analysis

Too low, may be including debris

Too high, cells excluded

Maximum Diameter

15 to 50 µm

1 to 60 µm

More cells identified

Less cells identified

Software is excluding large cells (circled blue)

Clumps of cells are included

Too low, may be excluding cells

Clumps of cells included

Cell Sharpness

5 to 25

0 to 100

Less cells identified

More cells identified

Software is excluding "fuzzy" cells

Unwanted debris is being picked up

Set too high may cause dead cell to be excluded and alter the percent viability.

Defines whether identified cells are viable or dead

Viable Cell Spot Brightness

40 to 60%

0 to 95%

More cells identified as dead

More cells identified as viable

Viable cells are identified as dead

Dead cells are identified as viable

Too low, may start identifying dead cells as live

Too high, may start identifying live cells as dead

Viable Cell Spot Area

3 to 12%

0 to 95%

More cells identified as dead

More cells identified as viable

Viable cells are identified as dead

Dead cells are identified as viable

Too low, may start identifying dead cells as live

Too high, may start identifying live cells as dead

Defines whether there is a cell present or not

Minimum Circularity

0 to 0.60

0 to 1.00

More irregular shaped dead cells will be excluded

Less irregular shaped dead cells will be excluded

Unwanted irregular shaped debris are being picked up

Too low, may be capturing unwanted debris

Too high, may start excluding cells

Decluster Degree

None, Low to Medium

N/A

More cells identified

Less cells identified

Cells in clusters are being missed

Single cells are being identified as 2 or more cells

Too low, may be missing cells in clusters

Too high, may over decluster by annotating single cells as 2 or more cells

 

Cell Sharpness

Cell sharpness is a measure of cell edges ranging from 0-100. Decreasing the value allows for fuzzier objects to be identified as cells. Increasing the sharpness will eliminates fuzzier cells from the cell count.

Viable Cell Spot Brightness

Viable Cell Spot Brightness measures the brightness of the center of the cells to determine whether the cell is viable or dead (green or red annotation). At high values cells with bright white centers are counted as viable (viability will decrease). At low values cells with grey centers will be counted as viable (viability will increase). It is important to check annotation to determine if Viable Cell Spot Brightness is set correctly.

Viable Cell Spot Area

Viable Cell Spot Area is a percentage of the white area of a cell used to determine if the cell is viable or dead. A high value may cause some viable cells to be counted as dead. It is normally not necessary to adjust this parameter.

Minimum Circularity

This parameter is used to eliminate debris. Assume "1" is a perfect circle.

Decluster Degree

The declustering degree defines intensity of declustering clumps of cells. None will not decluster any clumps of cells - Good for samples with cells that are very long and contain no cell clumps. Low is good for samples with clumps of 2-3 cells. Medium is good for samples with some clumps of with more than 3 cells. High is good for yeast cells.