![]() ![]() I hope this helps a bit! Just let us know… we are here to help. ![]() Introduction into Macro Programming page of the wiki.A helpful workshop on Scripting with Fiji - the slides are here.writing macro code - here are some other helpful links: MorphoLibJ plugin - another great tool for segmentation that comes with Fiji, providing more options/techniques… comes with Morphological Segmentation toolįor Scripting - ie.If you are just getting started, we recommend downloading/using Fiji. NOTE: Fiji is Just ImageJ - it is simply a distribution of ImageJ that comes with a bunch of plugins bundled - ready for you to use out-of-the-box. Trainable Weka Segmentation (TWS) plugin and it is scriptable via macro code - a great tool for segmentation that comes directly with Fiji.“Segmentation in Fiji” workshop and corresponding slides.Principles page - collection of principles for the entire image analysis process, from acquisition to processing to analysis.“Introduction to Fiji” workshop and corresponding slides- worth the time to get a solid intro.Powerful Fiji bundles together many popular and useful ImageJ plugins for image analysis into one installation, and automatically manages their dependencies and updating. ImageJ wiki - the best place to learn everything about ImageJ/Fiji!! Fiji is easy to use and install - in one-click, Fiji installs all of its plugins, features an automatic updater, and offers comprehensive documentation.Too - which are the ‘foci’ that you wish to count? The single bright spots? Or more?Īnd being new to ImageJ - no worries there! Here are some really helpful links to get you started: You have another nuclei-specific marker (DAPI or such?) for these images? That would be ideal… to first delineate (ie - segment) your nuclei with a more consistent (across all cells) marker such as DAPI and then use those ROIs to search for punctate/foci staining within. ![]()
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