Merge pull request #1 from 4ever2/project-setup

Project setup

.gitignore

@@ -0,0 +1,143 @@
+### Eclipse ###
+.metadata
+bin/
+tmp/
+*.tmp
+*.bak
+*.swp
+*~.nib
+local.properties
+.settings/
+.loadpath
+.recommenders
+
+# External tool builders
+.externalToolBuilders/
+
+# Locally stored "Eclipse launch configurations"
+*.launch
+
+# PyDev specific (Python IDE for Eclipse)
+*.pydevproject
+
+# CDT-specific (C/C++ Development Tooling)
+.cproject
+
+# CDT- autotools
+.autotools
+
+# Java annotation processor (APT)
+.factorypath
+
+# PDT-specific (PHP Development Tools)
+.buildpath
+
+# sbteclipse plugin
+.target
+
+# Tern plugin
+.tern-project
+
+# TeXlipse plugin
+.texlipse
+
+# STS (Spring Tool Suite)
+.springBeans
+
+# Code Recommenders
+.recommenders/
+
+# Annotation Processing
+.apt_generated/
+.apt_generated_test/
+
+# Scala IDE specific (Scala & Java development for Eclipse)
+.cache-main
+.scala_dependencies
+.worksheet
+
+# Uncomment this line if you wish to ignore the project description file.
+# Typically, this file would be tracked if it contains build/dependency configurations:
+#.project
+
+### Eclipse Patch ###
+# Spring Boot Tooling
+.sts4-cache/
+
+### Java ###
+# Compiled class file
+*.class
+
+# Log file
+*.log
+
+# BlueJ files
+*.ctxt
+
+# Mobile Tools for Java (J2ME)
+.mtj.tmp/
+
+# Package Files #
+*.jar
+*.war
+*.nar
+*.ear
+*.zip
+*.tar.gz
+*.rar
+
+# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
+hs_err_pid*
+replay_pid*
+
+### MATLAB ###
+# Windows default autosave extension
+*.asv
+
+# OSX / *nix default autosave extension
+*.m~
+
+# Compiled MEX binaries (all platforms)
+*.mex*
+
+# Packaged app and toolbox files
+*.mlappinstall
+*.mltbx
+
+# Generated helpsearch folders
+helpsearch*/
+
+# Simulink code generation folders
+slprj/
+sccprj/
+
+# Matlab code generation folders
+codegen/
+
+# Simulink autosave extension
+*.autosave
+
+# Simulink cache files
+*.slxc
+
+# Octave session info
+octave-workspace
+
+### VisualStudioCode ###
+.vscode/*
+!.vscode/settings.json
+!.vscode/tasks.json
+!.vscode/launch.json
+!.vscode/extensions.json
+!.vscode/*.code-snippets
+
+# Local History for Visual Studio Code
+.history/
+
+# Built Visual Studio Code Extensions
+*.vsix
+
+### VisualStudioCode Patch ###
+# Ignore all local history of files
+.history
+.ionide

README.txt → README.md

@@ -1,5 +1,7 @@
+# ImDecorr
+
 A detailled description of the method can be found in :+ 
-Descloux, A., K. S. Gru�mayer, and A. Radenovic. Parameter-free image 
+Descloux, A., K. S. Gru�mayer, and A. Radenovic. Parameter-free image 
 resolution estimation based on decorrelation analysis.
 Nature methods (2019): 1-7.
 
@@ -8,46 +10,42 @@ If this software has been usefull to your research, please consider citing
 https://doi.org/10.1038/s41592-019-0515-7
 
 -------------------
-This README.txt file should be accompanied by
+This README.txt is accompanied by
 
-* The plugin
-ImageDecorrelationAnalysis.jar in ijplugin folder
+* The plugin [ImageDecorrelationAnalysis_plugin.jar](ijplugin/ImageDecorrelationAnalysis_plugin.jar) in ijplugin folder
 
-* A demonstration dataset
-test_image.tif
+* A demonstration dataset: [test_image.tif](examples/test_image.tif).
 This data set consists in a confocal and a STED image of COS7 microtubules labelled with alexa594 combined in a single stack
 
-* A copy of the licence
-LICENSE.txt
+* A copy of the licence: [LICENSE](LICENSE)
 
-* A Matlab script
-main_imageDecorr.m
+* A Matlab script [main_imageDecorr.m](matlab/main_imageDecorr.m)
 
-* Matlab functions in a folder required by main_imageDecorr.m for image decorrelation analysis
+* Matlab functions in a [folder](matlab/funcs/) required by `main_imageDecorr.m` for image decorrelation analysis
 funcs
 
--------------------
-System requirements
 
-ImageDecorrelationAnalysis_plugin.jar will require a running installation of ImageJ
+## System requirements
+
+[ImageDecorrelationAnalysis_plugin.jar](ijplugin/ImageDecorrelationAnalysis_plugin.jar) will require a running installation of ImageJ
 Full instruction for the installation of ImageJ can be found at:
 https://imagej.nih.gov/ij/download.html
 
 The plugin requires ImageJ 1.48 or higher (tested for 1.48 to 1.52)
-ImageJ version number can be found under: Help -> About ImageJ...
+ImageJ version number can be found under: `Help -> About ImageJ...`
 
 Matlab functions were developped using 64bits Matlab R2017b
 
--------------------
-Installation guide
 
-Copy the file ImageDecorrelationAnalysis_plugin.jar in your ImageJ plugins folder (.../ImageJ/plugins)
-Restart ImageJ and the plugin will appear in the plugin list, under: Plugins -> ImageDecorrelationAnalysis
+## Installation guide
 
--------------------
-Demo
+Copy the file [ImageDecorrelationAnalysis_plugin.jar](ijplugin/ImageDecorrelationAnalysis_plugin.jar) in your ImageJ plugins folder `(.../ImageJ/plugins)`
+Restart ImageJ and the plugin will appear in the plugin list, under: `Plugins -> ImageDecorrelationAnalysis`
 
-Open the image of interest in ImageJ and make sure it is the active window. Before running the analysis, it is important to set the image pixel size and units (Image -> Properties� -> Unit of length, Pixel width and pixel height). If empty or not defined, the plugin will return the resolution in pixel.
+
+## Demo
+
+Open the image of interest in ImageJ and make sure it is the active window. Before running the analysis, it is important to set the image pixel size and units (Image -> Properties� -> Unit of length, Pixel width and pixel height). If empty or not defined, the plugin will return the resolution in pixel.
 Click on compute and once the analysis is done, results are added to the main results table.
 
 The plugin supports multidimensional stacks of any bit depth. If a RGB image is supplied, it will be automatically converted to grayscale. The plugin also supports rectangular ROI, which allows to repeat the analysis on sub-regions and check the consistency of the estimate over the whole image.
@@ -56,25 +54,24 @@ The settings panel is composed of 4 optional parameters of the computation, spec
 
 We also provide additional processing options in the form of 3 check-boxes:
 
-*Do plot:
+* Do plot:
 If checked, plot all the computed curves and results.
 
-*Batch stack:
+* Batch stack:
 If checked, process all the frames, slices and channel of the current image. If do plot is also checked, all the curves for all the images will be plotted.
 
-*Batch folder:
-If checked, the user will be asked to select a folder containing images. All images are then opened, processed and the result table is automatically saved in the selected folder as a .csv file. Again, if �do plot� is checked, all the curves will be plotted.
+* Batch folder:
+If checked, the user will be asked to select a folder containing images. All images are then opened, processed and the result table is automatically saved in the selected folder as a `.csv` file. Again, if "do plot" is checked, all the curves will be plotted.
 
--------------------
-Instructions for use
+
+## Instructions for use
 
 1. Open ImageJ
 
-2. Go to Plugins -> ImageDecorrelationAnalysis
+2. Go to `Plugins -> ImageDecorrelationAnalysis`
 A window will open with default settings already set
 
-3. Open the demonstration data set
-demo_COS7_a-tub_abberior_star635_confocal_STED.tif
+3. Open the demonstration data set `demo_COS7_a-tub_abberior_star635_confocal_STED.tif`
 
 4. Click on Compute