baby.preprocessing.SegmentationFlattening

class baby.preprocessing.SegmentationFlattening(filename=None)

Bases: object

Methods

__call__(filled_stack, info)

Call self as a function.

addGroup(name[, lower, upper, budonly, focus])

Add a new cell group to this flattener

addTarget(name, group, prop[, nerode, ...])

Add a new prediction target to this flattener

format_focus_assignment

getGroupTargets

getTargetDef

load

names

save
__init__(filename=None)

Methods

__init__([filename])

addGroup(name[, lower, upper, budonly, focus])

Add a new cell group to this flattener

addTarget(name, group, prop[, nerode, ...])

Add a new prediction target to this flattener

format_focus_assignment(areas, focusNums, ...)

getGroupTargets(group[, propfilter])

getTargetDef(name)

load(filename)

names()

save(filename)

addGroup(name, lower=1, upper=inf, budonly=False, focus=None)

Add a new cell group to this flattener

Parameters

  • name – a unique name to identify this group

  • lower – the lower size threshold (in pixels) of cells to include in this group

  • upper – the upper size threshold (in pixels) of cells to include in this group

  • budonly – whether to limit this group to cells annotated as buds

  • focus – a float specifying the focal plane that this group should correspond to. Cells with a focus annotation will be allocated to the group with the closest focal match.

addTarget(name, group, prop, nerode=0, ndilate=0, focusStacks=[])

Add a new prediction target to this flattener

Parameters

  • name – a unique name to identify this target

  • group – the name identifying the cell group from which this target should be generated

  • prop –

    the type of mask that should be generated for this target. Valid values are currently: - ‘filled’: True for all edge and interior pixels in the specified

    group, False otherwise;

    • ’edge’: True for all edge pixels of cells in the specified group, False otherwise;

    • ’overlap’: True for all pixels corresponding to at least two cells in the specified group, False otherwise;

    • ’interior’: True for all pixels

    • ’filledsum’: The integer number of cells present at each pixel;

    • ’budneck’: For all cells in this group, if a mother has been annotated, then set to True those pixels where the daughter overlaps with a dilated version of its mother

  • nerode – the number of erosions that should be applied for generation of this target.

  • ndilate – the number of dilations that should be applied for generation of this target.

  • focusStacks – a list of floats specifying focal planes. If non-empty, this is shorthand for creating a new group for each of the specified focal planes (copying the properties of the specified cell group) and creating a corresponding target.