Playing with Phase and Magnitude

 

In this series dedicated to the Fourier Transform, it is important to understand the role played by magnitude (or amplitude) and phase in an image...

Model bias in cryo-EM - Einstein from noise

 

 
 
In the article of Maxim Shatsky et al.  entitled "A Method for the Alignment of Heterogeneous Macromolecules from Electron Microscopy" (J Struct Biol. 2009, 166(1): 67–78. doi:10.1016/j.jsb.2008.12.008.), the authors show that pure noise images aligned to a reference image give an average image resembling the reference. This is a perfect example of the model bias occurring during the 2D classification step. Let's do it!!!

Case study: The target

In this case study, we want to count the number of points obtained in this shooting session.

Normal Map of a sphere using ImageJ

 A small script for creating a normal map of a sphere using ImageJ.

Dataset for Machine Learning

Dataset for experimenting machine learning methods.

Analysis of an Antibiogram

In this case study based on the article entitled Single bacterial super-clone behind world epidemic of drug-resistant E. coli of M. McCarthy [Link], there is an image of an Antibiotic Susceptibility Testing and the question is: "Is it possible to automatically detect the wafers and the inhibitory areas?"...

ML Toolkit

I developed a tiny Machine Learning (ML) toolkit written in JavaScript containing helper functions...

k-Nearest Neighbor Classifier

First try with one of the simplest classifier: The k-Nearest Neighbor Classifier...

TDS API

Here is the API (Application Programming Interface) of the TDS (Tiny DataSet helper class) for the Machine Learning examples

Tiny Dataset Toolkit in JavaScript

I developed a tiny toolkit written in JavaScript containing helper functions to manipulate data...

Dataset and Features

To feed a learner of Machine Learning (ML), we need data. But, rather than using image pixels, it is much more powerful to use ImageJ measurements (or features in the ML jargon) ...

Dataset for ML

A new series about Machine Learning (ML) and Image Processing with ImageJ. First we need to create a dataset suitable for machine learning...

Perspective Transform

Among the various geometric transformations, the Perspective transform is very useful. By default, this transform is not available in Image > Transform. However, it is very easy to implement such a tool...

Functions in ECMAScript

Functions have a central role in JavaScript (ECMAScript 2015+),this is important to know how to use them...

Loops

Repeating tasks in a script is the most important part when programming. This process is done using a specific statement: the loop. In JavaScript, you can use while, for (..), for (.. in ..), for (.. of ..).

Conditionals

Using conditionals in a script is a way to execute different parts of a code depending of the result of a condition. What is a condition, the operators (comparison and logical)?

Read/Write Pixels in a RGB image

Thanks to the methods of the class ImageProcessor [see Post], it is possible to read and write pixels in an image.

Read and Write Pixels in Grayscale Images

Thanks to the methods of the class ImageProcessor [see Post], it is possible to read and write pixels in an image.

Variables in ECMAScript

With the new version of JavaScript (ECMAScript 2015+), the variables are now defined by three distinct keywords: var, let, and const. Why? That's what we'll see in this post.

ImageJ and ECMAScript 6

With the last update of ImageJ 1.51r, it is possible to use Java 9 and its new JavaScript engine Nashorn with ECMAScript 6 functionalities.... and that's a great news!! See how to do that...