Extracting fluorescence values Extracting fluorescence values in an .h5 file in the BigDataViewer format around given coordinates

Source: R/getFluo.R

Extracting fluorescence values Extracting fluorescence values in an .h5 file in the BigDataViewer format around given coordinates

getFluo(H5_path, Spots_df, x_px = x_px, y_px = y_px, z_px = z_px,
  timepoint = FRAME, cubeSize = 5)

Arguments

H5_path

path to the H5 file used to create the mamut.xml file
Spots_df

dataframe containing on each rows spots locations at which to retrieve fluorescent values
x_px

name of the column with x coordinates in pixels in Spots_df
y_px

name of the column with y coordinates in pixels in Spots_df
z_px

name of the column with z coordinates in pixels in Spots_df
timepoint

name of the column where the timepoints or frames are stored
cubeSize

half the length of the cube side length. By default the cube is 10x10x10 pixels.

Value

a list of length equal to the number of timepoints. For each timepoint, values of fluorescence around each spot location

Note

Many thanks to Dr. Mike Smith for his help on this function.