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Guillaume Raffy 4932427663 display sequence will now allow the loading of sequences with missing frames 
Sequences with missing frames are not uncommon in the raw images that were collected at soleil. I beleive that these missing frames are caused by the sequence captures that are stopped, resting in missing frames at the end compared to what was planned....

fixes #10
 		2022-01-26 22:25:42 +01:00
doc added notes taken in past 2 meetings related to lipase 2022-01-25 07:45:38 +01:00
scripts added comments 2020-07-08 15:41:17 +02:00
src display sequence will now allow the loading of sequences with missing frames 2022-01-26 22:25:42 +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
Jenkinsfile and another attempt... 2020-04-10 17:53:01 +02:00
LICENSE Initial commit 2019-03-07 10:22:51 +01:00
Makefile display sequence will now allow the loading of sequences with missing frames 2022-01-26 22:25:42 +01:00
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