This use case demonstrates how to detect the inside and outside area of cells, calculate the intensity ratio per cell, median of all cells and other summary statistics.

Figure 783. Original image.

Figure 784. Analysis definition.

To correctly detect cells on the DAPI channel, Shading correction is applied, Bright Spots are detected and Circular Open is used.

Figure 785. DAPI cells.

Make Inside & Ring node is applied to split each cell into two parts – the inner part (Inside) and the membrane (Ring).

Figure 786. Make Inside & Ring node.

Figure 787. Cell inside.

Figure 788. Cell ring.

Sum Intensity is measured in the cell insides and cell rings under the FITC channel. Nodes in our definition are renamed from “SumIntensity” to “InsideSumIntensity” and “RingSumIntensity” respectively.

Figure 789. Sum Intensity for the cell insides.

Figure 790. Sum Intensity for the cell rings.

These two records are joined together by their “ObjectId” using the Join Records node.

Figure 791. Join Records results.

A new column named “InsideToRingIntensity” is created using a custom JavaScript where the records from the “InsideSumIntensity” column are divided by the records from the “RingSumIntensity” column resulting in the intensity ratio per each cell.

Figure 792. JS Create Column node.

Figure 793. Resulting JavaScript column.

Finally, all the records are summarized using the Aggregate Rows node to show the selected statistics.

Figure 794. Aggregate Rows node.

Figure 795. Resulting statistics.