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Guillaume Raffy 442645d710 prevented the console window to appear and diaply messages that are irrelevant to users. 
To do this, I turned log messages into debug messages. While doing so, I also added an IJLogger that is able to log messages on imagej console, in case we need it in the future
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doc added notes taken in past 2 meetings related to lipase 2022-01-25 07:45:38 +01:00
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src prevented the console window to appear and diaply messages that are irrelevant to users. 2022-01-25 14:53:37 +01:00
tests imagej's headless regression no longer causes tests to fail (as these failures only happen in headless mode, see issue #6) 2022-01-25 07:44:23 +01:00
.gitignore imagej's headless regression no longer causes tests to fail (as these failures only happen in headless mode, see issue #6) 2022-01-25 07:44:23 +01:00
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README.md notes taken at the meeting of 10/07/2020 2020-11-03 15:58:51 +01:00

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 ImageJ Updater window, click on the Manage update sites button. This opens the Manage update sites window.
    • 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 (the directory that contains Fiji executable eg /home/graffy/soft/Fiji.app)
  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