FlowJo Data Analysis Software Operation

severe

Rare Cell Population Incorrectly Gated or Missed

Target rare immune cell subsets (e.g., dendritic cells, innate lymphoid cells, hematopoietic progenitors) appear overestimated or masked by abundant terminally differentiated cells. Gating on single markers yields incorrect population percentages (e.g., 4.5% vs. true 1.2% DCs).

💡 4 · ✓ 4

moderate

Multiple Cell Populations When Expecting Single Population

Flow cytometry plots display two or more distinct cell populations where only one homogeneous population was expected. A second population often appears at approximately twice the fluorescence intensity of the primary population.

💡 3 · ✓ 3

moderate

Autofluorescence Complicating Cell Population Gating Strategy

Difficult to establish clear gates between positive and negative populations. Autofluorescent cells appear in unexpected regions of scatter plots, creating ambiguous boundaries and potential misidentification of cell populations.

💡 4 · ✓ 5