extraction.core.functions.cell

Base functions to extract information from a single cell.

These functions are automatically read by extractor.py, and so can only have the cell_mask and trap_image as inputs. They must return only one value.

They assume that there are no NaNs in the image.

We use the module bottleneck when it performs faster than numpy: - Median - values containing NaNs (but we make sure this does not happen)

Functions

area(cell_mask)	Find the area of a cell mask.
conical_volume(cell_mask)	Estimate the volume of the cell.
eccentricity(cell_mask)	Find the eccentricity using the approximate major and minor axes.
max2p5pc(cell_mask, trap_image)	Find the mean of the brightest 2.5% of pixels in the cell.
max5px(cell_mask, trap_image)	Find the mean of the five brightest pixels in the cell.
mean(cell_mask, trap_image)	Find the mean of the pixels in the cell.
median(cell_mask, trap_image)	Find the median of the pixels in the cell.
min_maj_approximation(cell_mask)	Find the lengths of the minor and major axes of an ellipse from a cell mask.
spherical_volume(cell_mask)	Estimate the volume of the cell.
std(cell_mask, trap_image)	Find the standard deviation of the values of the pixels in the cell.
volume(cell_mask)	Estimate the volume of the cell.