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Welcome to the Fiji-Tools-for-HCS wiki!

Purpose

This wiki supports the documentation of Fiji macros and plugins that have been created to process and analyse images that are come from automatic microscopes and/or need some automated processing. This page was created by MPI-CBG staff HT-TDS and is open to host all useful tools in the field of high-content screening (HCS).

Installation

To use the Fiji-Tools-for-HCS you need to install Fiji with the update site 'Fiji-Tools-for-HCS'.
Installation details here...

Content Overview

Currently, all tools are Fiji macros (Imagej macro language) and suppose to run with the latest version of Fiji. A set of plugins (written in Java) is currently under development and suppose to extend the functionalities within the macro language. This plugin is called "FijiToolsForHCSplugin". The macros "Fiji-Tools-for-HCS" are sorted into categories. Details you will find on each macro wiki site.

Automated Microscope Tools

• ArrayScan RGB merger (tbd)
• CV7000 Create Illumination Correction Images From Dye Images
• CV7000 Create Illumination Correction Images From Many Images
• CV7000 Illumination Correction (tbd)
• CV7000 Create Plate Montage (tbd)
• CV7000 Image Stitcher (tbd)
• CV7000 Make Time Lapse Movies
• CV7000 Z-Projection
• Opera Channel Splitter MaxProjection (tbd)
• Opera RGB merger (tbd)

Cell Analysis Tools

• Cell Classifier
• Line Scan Cells
• Line Scan 3D Cells

File Conversion

• Leica .lif to .tif
• Leica .lsm to .tif
• Olympus .oib to .tif

Fish Embryo Screen

• Opera Stack Montage for Fish
• Segment2D in ROI
• Select ROI for Segmentation

Image File Filter

• ImageFileFilter Open List of Images
• ImageFileFilterRegEx Open List of Images (on ToDo list)
• ImageFileFilter Manual Counter

Development & Code

• Check Fiji Installation
• Useful Functions for Fiji Macros

this wiki is still under construction (for quick questions send email to the email address below...)

Code

The macros and plugins are hosted here at GitHub and at ImageJ server.

Access

Feel welcome to contact us (stoeter at mpi-cbg.de) if you want to contribute to this project, have suggestions, found bugs, or want to be able to edit the wiki (please login and notify stoeter at mpi-cbg.de so that editing permissions can be given).

:Category:Input-Output :Category:Fish-Embryo-Screen :Category:Automated-Microscope-Tools :Category:Misc