lipase/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 and quit Fiji
3. Install lipase
    - lipase is released as a package named "lipase-<lipase-version>.zip". This package can be build 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

## Notes

http://imagejdocu.tudor.lu/doku.php?id=plugin:analysis:microscope_image_correlation_spectroscopy:start
Initial commit 2019-03-07 10:22:51 +01:00			`# lipase`

made a proper documentation 2019-03-29 15:58:18 +01:00			`An image processing software suite for the project lipase (Véronique Vié, Institut de Physique de Rennes)`
added documentation 2019-03-29 15:13:54 +01:00
Reorganised directories to ease identification of sequences. The sequence id now cantain the id of the image capture campaign 2019-04-01 12:26:37 +02:00			`This software suite is developed as a python script for fiji (an image processing package based on imageJ).`
made a proper documentation 2019-03-29 15:58:18 +01:00
			`## 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/`
added modifications made on 09/04/2019 2019-07-16 11:12:39 +02:00			`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`
now that lipase is realeased as a package, I updated the user documentation accordingly 2019-10-07 12:25:01 +02:00			`- 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 build 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`
added modifications made on 09/04/2019 2019-07-16 11:12:39 +02:00
			`## Notes`

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