Nuclei Module
This module performs nuclei detection, segmentation, and cytometry.
These include the following subcommands:
detect : detect all nuclei in image
segment : segment all detected nuclei
fluorescence : measure fluorescence for each cell
gate : assign cell-type labels by fluorescence thresholding
morphology : compute morphological features of segmented nuclei
name : assign names to each cell-type
- scout.nuclei.calculate_mfi(input)
Calculate the Mean Fluorescence Intensity (MFI) for input list of nucleus-centered samples
- Parameters
input (list) – List of ndarrays containing image intensities near nuclei
- Returns
output – 1D array of MFIs for each nucleus
- Return type
ndarray
- scout.nuclei.calculate_stdev(input)
Calculate the standard deviation for input list of nucleus-centered samples
- Parameters
input (list) – List of ndarrays containing image intensities near nuclei
- Returns
output – 1D array of standard deviations for each nucleus
- Return type
ndarray