dwaithe

//ImageJ macro written by Dominic Waithe. (c) 2017.
//To be used on three channels of an image file.

//Output:
	//prints to log for each cell something like this: Cell Number: 	 270  	Foci Count CH1:	 7 	Foci Count CH2: 4 	 particles within distance 5
	//outputs image

//Parameters for the code

	//DAPI channel. Used to find the areas.

dwaithe

//ImageJ macro written by Dominic Waithe for Caroline Scott. 2017.
//This macro uses the Hough circlular transform to count the number of cells present.
//Works very well, but artefacts on sample will lower accuracy.


///Parameters
//Radii to focus the hough-transform on
r_start = 6; //radii minimum size
r_stop = 8; //radii maximum size.
edge_mag = 70; //Threshold for edge magnitude, the lower this value the more of the edges will be captured.

dwaithe

// 2D Gaussian fitting example with rough feature identification.
//////////////////////////////////////////////

// Written by Dominic Waithe. University of Oxford. Follow on Twitter at @dwaithe. Or https://github.com/dwaithe
// Copyright (c) 2016 Dominic Waithe. See license at bottom of file.

//// Details:
// Fiji/ImageJ. Just make sure its up-to-date. Tested on v 1.49. 
// This script includes a rough feature detection and then fine 2D Gaussian algorithm to fit Gaussians within patches regions.
// This macro is special because the ImageJ/Fiji curve fitting API only supports 1-D curve. I get around this by...

dwaithe

//File converter code. Converts lsm files to ome.tiff from and input folder to and output folder.
//Written by Dominic Waithe for Heinrich Klose (2017).

//You need to change these values to your folders of choice.
input_dir = "set/path/to/input/folder";
output_dir = "set/path/to/output/folder";


//Processing code begins:

dwaithe

/Macro written by Dominic Waithe for Victoria Zilles, Erdinc Sezgin and Falk Schneider.
//Measure FWHM at multiple points along a user-defined line
//Fits intensity profile using Gaussian Fitting
//Outputs data from STED and CONFOCAL in log.
//Dominic Waithe 2016, University of Oxford.

//Find the coordinates of the selection.
getSelectionCoordinates(xr, yr);
//Add the coordinates to the roi manager.
roiManager("Add");

dwaithe

from scipy.ndimage import map_coordinates
import numpy as np

def rigid_transform_3d(input_im, alpha,beta,gamma,xt,yt,zt,order=2):
    """
    Function which performs a rigid-body transformation on volumetric intensity data:
    
    -- example usuage --
    %pylab inline #in jupyter or ipython include this for the visualisation.
    inw = np.zeros((30,35,50))