Pipeline Functions

Created on Thu Jan 30 10:29:52 2020

@author: jlbraid

pipelines.FMpipeline(imagepath, savepath, n=None, f=None, numCols=None, numRows=None, savesmall=False, imgtype='')

Performs full-size module image processing steps, including

lens correction, planar indexing, and cell extraction, if desired.

Lens correction is performed if n and f are provided. n and f can be found with the GetLensCorrectParams function. Cells are extracted if numCols and numRows are provided.

Args:

imagepath (str): path to a raw image savepath (str): folder path for saving output numCols (int): number of cells across in module image numRows (int): number of cells down in module image savesmall (bool): Save a smaller .jpg version of the planar indexed

image with True. Default is False.

imgtype (str): ‘UVF’ UV Fluorescence Image

‘gradient’ for unequal intensity across the image ‘lowcon’ low contrast between cell and background

or PL images without background subtraction

Returns:

pipelines.GetLensCorrectParams(imagepath, imgtype='')

Automatically detects lens correction parameters for an image

using linear fitting of the module edges.

Args:

imagepath (str): path to a raw image imgtype (str): ‘UVF’ UV Fluorescence Image

‘gradient’ for unequal intensity across the image ‘lowcon’ low contrast between cell and background

or PL images without background subtraction

Returns:

n,f (float): lens correction parameters

pipelines.MMpipeline(imagepath, savepath, numCols, numRows, stitch=False, imgtype='')

Performs minimodule image processing steps, including cell extraction,

planar indexing, and re-combination of cell images into a module image, if desired.

Args:

imagepath (str): path to a raw image savepath (str): folder path for saving output numCols (int): number of cells across in module image numRows (int): number of cells down in module image stitch (bool): True if output image with cell-level images stitched

together is desired. Default is False

imgtype (str): ‘UVF’ UV Fluorescence Image

‘gradient’ for unequal intensity across the image ‘lowcon’ low contrast between cell and background

or PL images without background subtraction

Returns: