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lipase
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Projet lipase porté par vvie
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Guillaume Raffy 608fefce0a more work towards graffy/lipase#3 : replaced circle kernels with circle arc kernels, as circle arcs are needed to compute the variance of the image along the circles. Note that at the moment the code doesn't yet compute the variance. 
This commit is not intended to change the radial profile image.
 		2020-04-07 14:15:54 +02:00
doc - added user documentation for lipase imagej plugins 2020-03-31 18:57:36 +02:00
scripts - fixed bug (introduced in my last commit) that broke release_lipase_package.bash 2020-04-01 12:00:57 +02:00
src more work towards graffy/lipase#3 : replaced circle kernels with circle arc kernels, as circle arcs are needed to compute the variance of the image along the circles. Note that at the moment the code doesn't yet compute the variance. 2020-04-07 14:15:54 +02:00
tests now there is an image processing to compute the radial profile (needed for graffy/lipase#3). 2020-04-06 16:35:28 +02:00
.gitignore started to translate matlab telemosToolbox's preprocessing functions into jython so that they can benefit from fiji framework 2019-07-17 16:56:05 +02:00
Jenkinsfile added doc generation in jenkins continuous integration 2020-03-18 16:42:14 +01:00
LICENSE Initial commit 2019-03-07 10:22:51 +01:00
Makefile added a function that creates an image containing a circle 2020-04-02 15:52:43 +02:00
README.md forgot to add this in my last 2 commits 2020-04-01 12:01:38 +02:00

README.md

lipase

An image processing software suite for the project lipase (Véronique Vié, Institut de Physique de Rennes)

This software suite is developed as a python script for fiji (an image processing package based on imageJ).

What it does

As the development is at its early stages, it does not much at the moment:

  • loads a sequence of images into fiji in the form of an hyperstack (5d images : width, height, depth, channels, time)

How to install

  1. make sure that fiji is installed on your computer. If not, get it from https://fiji.sc/
  2. make sure that fiji has the IJ-OpenCV-plugins
    • in Fiji, select the Help->Update... menu item
    • in the Manage update sites window, tick the IJ-OpenCV-plugins (URL = http://sites.imagej.net/IJ-OpenCV/) if it's not ticked.
    • click the close button of the Manage update sites window
    • click Apply changes button in the ImageJ Updater window
    • wait until the plugins are installed and quit Fiji
  3. Install lipase
    • lipase is released as a package named lipase-<lipase-version>.zip. This package can be built from sources using the make package command, provided you have all the build tools on your machine (make, javac, zip).
    • simply unzip the package lipase-<lipase-version>.zip in Fiji root directory
  4. launch fiji and check that you have lipase tools in the menu Plugins/Ipr/Lipase

How to use

see lipase-manual.pdf (this document can be built from sources using the make doc command, provided you have all the build tools on your machine (make, pdflatex, imagemagick)

Notes

http://imagejdocu.tudor.lu/doku.php?id=plugin:analysis:microscope_image_correlation_spectroscopy:start