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Projet lipase porté par vvie
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Guillaume Raffy e8523efd18 added nearly all of estimate_white's post processing (particles removal) 
As a result, the implementation of estimate_white is getting closer to completion. However, the performance of fiji's gray morphology is very poor, which makes it practically unusable with the default settings provided in the original code (estimateWhiteFluoImageTelemos)

Bug 2623 - Faire un traitement automatique pour les images du projet lipase
 		2019-09-13 15:15:01 +02:00
scripts improved speed and reliablility of jenkins build by replacing the download of the fiji package with the use of a predownloaded version. 2019-07-17 19:29:26 +02:00
tests added nearly all of estimate_white's post processing (particles removal) 2019-09-13 15:15:01 +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 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
LICENSE Initial commit 2019-03-07 10:22:51 +01:00
Makefile added basic jenkins file to automate the build of hello 2019-03-07 10:56:01 +01:00
README.md added modifications made on 09/04/2019 2019-07-16 11:12:39 +02:00
catalog.py 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
ijopencv-tester.py fixed pep8 2019-04-12 16:28:40 +02:00
lipase.py 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
preprocessing.py added nearly all of estimate_white's post processing (particles removal) 2019-09-13 15:15:01 +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 use

  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, then restart fiji
  3. launch fiji
  4. from fiji, click on File->new->script... The script window should appear.
  5. with the script window selected, choose the File->open... menu item.
  6. from the file browser that just appeared, locate and choose the file lipase.py from this repository, then click Open. You should see the script lipase.py appear in the script window
  7. The script is executed when you click on the script editor's run button.

Notes

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