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This repository contains macros, scripts and teaching material for quantitative image analysis using ImageJ Fiji and Python

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# General Macros for Fiji (ImageJ)

This collection of macros is to help with tricky or interesting problems using the image analysis package Fiji (ImageJ). For more information about Dominic and his projects please refer to his main [homepage](https://dwaithe.github.io/home/).

##### General Requirements:

Macros written for Fiji/ImageJ. If don't have Fiji, you can download  it here: imagej.net/Fiji/Downloads

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### Contents
- Macro script for fitting FWHM along a line. 
- Macro script for fitting 2D Gaussians (Diagonally covariant)
- Macro script for converting a folder of images to another format.

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### Macro script for fitting FWHM along a line. 
Script location in GIST: [WHM_along_line_v1.ijm](https://gist.github.com/dwaithe/2b9581324e3c8caf9238765ce50127fb).  
Example file to test script: [2.lif](https://drive.google.com/file/d/1mQ1yezSlPRWksWduzm6WNVTeg0uZU1Qs/view?usp=sharing).   
#### Description:  
A bulk FWHM measuring algorithm was designed and written using ImageJ macro language. Using the ImageJ interface the user defines a line using the Segmented line tool which follows the contour of the GUV to be measured. The algorithm is then run and will interpolate along the user-defined line and calculates points at regular intervals (3 pixel gap). At each interpolated point on the line a perpendicular lines is drawn 40 pixels in length and centred on the interpolated line. Along each of these perpendicular lines the intensity values are sampled and a Gaussian curve is fit using the ImageJ curve fitting plugin. The parameters of each curve are then output and the FWHM calculated for each curve (2*sqrt(2*log(2)*sigma), where sigma of Gaussian fit).

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### Macro script for fitting 2D Gaussians (Diagonally covariant)
Script location in GIST: [2D_GaussFit.ijm](https://gist.github.com/dwaithe/186f910ebf58f65ebd26ff4692b00ee3).   
Example file to test script:[2D_Gaus_sig4.png](resources/2D_Gaus_sig4.png).

with example file:

![alt text](https://raw.githubusercontent.com/dwaithe/generalMacros/master/resources/2D_Gaus_sig4.png "Example image")
![alt text](https://raw.githubusercontent.com/dwaithe/generalMacros/master/resources/example_output.png "Example output")

#### Description: 
This script includes a rough feature detection using the in built Find Maxima algorithm and then fine 2D Gaussian algorithm to fit Gaussians within square patch regions. This macro is special because the ImageJ/Fiji curve fitting API only supports 1-D curve. I get around this by linearising the equation. The equation is for isotropic (spherical) or anistropic (longer in x/y) diagonally covariant Gaussians but not fully covariant Gaussians (anisotropic and rotated), I will include that in another script. There are further instructions and parameters in the macro itself.
Based on https://en.wikipedia.org/wiki/Gaussian_function two-dimensional Gaussian function.

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### Macro for converting a folder of images to another format.
Script location in GIST: [file_converter.ijm](https://gist.github.com/dwaithe/526eb15b06fa88e4981d70d3c1a73b60). 
#### Description:
Simple example script which shows how to convert .lsm files from one folder into another folder and save as ome.tiff

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