Guillaume Raffy
e6217b38a3
The 2 available plugins are: - Define Raw Images Root: this plugin allows the user to tell lipase where the raw images are stored - Estimate White: this plugin allows the user to trigger the computation of a white image estimate for the given sequence and the given channel (the sequence id an the channel ids are currently hardcoded but it is of course planned to make it user selectable) These changes involved quite a lot of work: - added the support of a lipase user settings file to store user dependent things such as the location of the lipase raw images (to allow the user to use lipase plugins without having to specify the raw images locations again an again) - investigations on how to make different lipase plugins use a common lipase library: the library is packagesd into a jar file placed in Fiji/jars/lib, while the plugins (menu items) are placed into Fiji/plugins directory - investigations on fiji script parameters (for plugins input output) |
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| README.md | ||
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
- make sure that fiji is installed on your computer. If not, get it from https://fiji.sc/
- 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
- launch fiji
- from fiji, click on File->new->script... The script window should appear.
- with the script window selected, choose the File->open... menu item.
- 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
- The script is executed when you click on the script editor's run button.