CytelyDocs

Plots & gating

The building blocks of an analysis in the Data explorer: plots, gates, tables, and notes.

Scatter plots

Click Add scatter plot and pick an X and Y parameter - area, intensity, circularity, or any measured feature. Add as many plots as you need; each one is a lens on the same underlying detections.

Each point is one detected object, colored by group. In the example below, mean DAPI intensity is plotted against object area, and the two wells are overlaid in orange and blue.

Gates

Drag with the left mouse button on a scatter plot to draw a gate - a rectangle or polygon selection that defines a subpopulation. Move a gate by dragging its interior; resize it by dragging its edges.

A gate is named and reports how many objects it contains, both as an absolute count and as a share of the parent population - here 132 (2%) small, bright nuclei labelled "Dividing cells".

Scatter plot of mean DAPI intensity against area, with a polygon gate named Dividing cells containing 132 objects (2%).
A scatter plot with a polygon gate. The gate label shows its name and the number and percentage of objects it captures.

Plots downstream of a gate update to show only the objects it contains, so chaining gates lets you narrow to very specific populations step by step - for example, "all phagocytes → prey-positive phagocytes → high-intensity prey".

Plot shortcuts

  • Zoom - hold Space and scroll (or use a two-finger gesture on a touchpad) over a scatter plot to zoom in and out.
  • Change an axis range - drag directly on the axis you want to rescale.
  • Log scale - right-click an axis to switch it to a logarithmic scale.

Histograms

Click Add histogram and pick a parameter to see its distribution - useful for comparing intensities between subpopulations or across groups.

Histogram of max DAPI intensity showing object counts per intensity bin with a right-skewed distribution.
A histogram of max DAPI intensity. The y-axis is object count per bin, making skew and outlier tails easy to spot.

Bar charts

Click Add bar chart and pick a parameter to compare it across groups. Each bar is the group mean with error bars showing the standard deviation, and the individual objects are overlaid as jittered points so you can see the spread behind the summary.

Bar chart of mean object area for Well 1 and Well 2 with standard deviation error bars and jittered per-object points.
A bar chart comparing mean area between two wells. Error bars show standard deviation; each dot is a single object.

Bar charts respect the active gates, so gating first and then adding a bar chart compares only the population you selected.

Statistics tables

Click Add table and choose the parameters you want to summarize. Cytely reports mean, median, standard deviation, and object count (n) for the currently gated population, split by group.

Each metric is a row you can expand to break the numbers down per group, with the group colors matching the plots.

Statistics table listing area and max DAPI intensity with mean, median, standard deviation and n, with area expanded into Well 1 and Well 2 rows.
A statistics table. Expanding a metric splits mean, median, SD, and n by group.

Notes

Because Cytely datasets can be shared, it's worth annotating them. Add a free-form note with Add note to capture context, conditions, and interpretation next to the data.

Phagocytosis assay table

If your dataset contains phagocytosis data, click Add phagocytosis assay to add a table of assay-level metrics like iMOP and phagocytosis score.

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