Area Occupied

Area Occupied measures how much of the image the objects of one class cover: the covered area in pixels, in µm² (when the pixel size is known) and as a part of the image (0 to 1). Where objects of the class overlap, the shared pixels count once.

It is a measurement step: it runs once per image plane, after all objects of the image are found, and gives one value per plane - not one per object.

Parameters

Parameter	Description
ID	The step’s ID, unique in the project. It is given automatically (area_occupied_01, …) and starts the names of its values in the results.
Object Class	The objects whose area is measured. It must be set.

Measurements

Three values per image plane:

Measurement	Unit	Description
Area occupied	px²	The number of pixels at least one object of the class covers.
Area occupied	µm²	The same area in µm². No value when the image has no pixel size.
Part of the image occupied	0-1	The covered pixels divided by the pixels of the image.

The two Area occupied values differ by their unit; in the measurement pickers they read “area_occupied_01 · Area occupied (px²)” and “(µm²)”.

How it works

Only the pixels of the objects’ masks are counted, not their bounding boxes: a hole in an object is not covered. The masks are merged row by row, so a pixel covered by several objects counts once:

$$A = \Big|\bigcup_{o \in \text{class}} \text{mask}(o)\Big|, \qquad A_{\mu m^2} = A \cdot \frac{s_x \, s_y}{10^6}, \qquad \text{Part} = \frac{A}{N_{\text{image}}}$$

with $s_x, s_y$ the pixel size in nm and $N_{\text{image}}$ the number of pixels analysed: all tiles of the image (in a preview, the part that is shown).

Results

The values belong to the image plane, not to an object. In the List view they are under Columns › Measurements, named “area_occupied_01 · Area occupied”. With A row per: Images each image shows its own value; with A row per: Objects each object row shows the value of its image plane. In the Plate view a well gets the statistic over its images’ values; images left out are not counted.

The export option Measurements - one row per value writes measurements.csv / .xlsx with one row per value (image, plane, step, measurement, unit, key, value) - see Exporting Results.

Limitations

• One class per step. To measure several classes, add a step for each.
• Values are per plane; there is no total over a z-stack or a time-lapse.