Get colabelled cells data table. This is designed specifically to create a segmentation object from the imported raw files that are outputs from the batch_3D_MultiColocalization.ijm macro.

Get colabelled cells data table. This is designed specifically to create a segmentation object from the imported raw files that are outputs from the batch_3D_MultiColocalization.ijm macro.

Usage

get.colabeled.cells(
  coloc_table,
  image_A_objects,
  image_B_objects,
  volume = 25,
  euc_centroid_dist = 30,
  overlap = 0.5
)

Arguments

volume

(default = 25) Minimum threshold for colocalized volume in voxels.

euc_centroid_dist

(default = 30) Euclidean threshold in pixels between the centroid coordinates of two flagged overlapping objects. If this distance is exceeded, there will be an error message.

overlap

(default = 0.5) Minimum fraction of object volume overlap from image A (Ch2) with object from image B (Ch1). Fraction is of image A objects.

Value

returns segmentation object with x Y coordinates as an average of the centroid coordinates. The area will be replaced with the volume of the image A object. Intensity is also just replaced with the volume of the image A object.