graffy
/
lipase
1
0
Fork 0
Code Issues 2 Pull Requests Releases Wiki Activity
Projet lipase porté par vvie
91 Commits 1 Branch 1 Tag 901 KiB
Python 95.6%
Makefile 3.2%
Shell 1.2%
Go to file
Guillaume Raffy e8b1e331fe added a function that creates an image containing a circle 
this function will be used for to complete #3
 		2020-04-02 15:52:43 +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 added a function that creates an image containing a circle 2020-04-02 15:52:43 +02:00
tests added a function that creates an image containing a circle 2020-04-02 15:52:43 +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