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lipase
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Projet lipase porté par vvie
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Guillaume Raffy 463cd9d0d9 added sphinx settings in order to use sphinx to check the syntax of arguments 
I'm not planning at the moment to use sphinx to generate the user documentation, as latex seems richer....
 		2020-04-14 10:40:50 +02:00
doc added sphinx settings in order to use sphinx to check the syntax of arguments 2020-04-14 10:40:50 +02:00
scripts fixed bug that cause release_lipase_package.bash to not handle the case when the package is not in the current directory 2020-04-10 18:02:30 +02:00
src more work related to graffy/lipase#3: for each pixel, the profile of variance along the circle is now computed. This image basically measures the non-roundedness for each pixel. 2020-04-08 13:38:16 +02:00
tests allows the user to choose the location of the tests output data 2020-04-10 13:26:05 +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 and another attempt... 2020-04-10 17:53:01 +02:00
LICENSE Initial commit 2019-03-07 10:22:51 +01:00
Makefile fixed bug introduced today that caused the package file to not contain jars/Lib/fr.univ-rennes1.ipr.lipase.lib.jar 2020-04-10 17:21:12 +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