MM_Images_to_Hyperstack ĭescription: This Beanshell script runs in Micro-Manager, and replicates the basic functionality of our old 4d acquisition plugin running under ImageJ. This plugin automates the creation of a Hyperstack from the Metadata.txt file of a Micro-Manager dataset.and loads into a Virtual HyperStack window in ImageJ 1.53c and later. Download sample dataset and info file as a ZIP archive (33.6 Mb) To see how these work in practice, here is a small sample 4d movie with 8000 frames (20 focal planes, 400 time points) in xyctz format. Note: the AVI importer that uses direct ImageJ calls requires ImageJ 1.53c or later to allow xyctz as well as the default xyczt arrangement of 4d data. With Mac OS X, right-click on the ImageJ or Fiji application and execute "Show package contents…" to navigate to the correct folder. To use these plugins, place the toolset file somewhere in the ->macros->toolsets folder hierarchy in your ImageJ home directory to enable this functionality. I have written simple macros that read legacy text files with 4d information using Stanislav's routines for use with legacy 4d movies in xyctz format (typically single-channel movies). This means that files can be resaved into one of these formats from legacy datasets, salvaging old, non-raw 4d data. More importantly, files saved in widely used AVI and H264/MP4 formats can be imported this way. MOV files) work if the JPEG image codec was used. Some really old flattened (i.e., non-resource fork-based. ![]() I have tested these plugins under Mac OS X 10.15 (Catalina), Windows 10 (64-bit) and Ubuntu Linux 20 (64-bit). Restart ImageJ, and then you should able to run the Import and Export plugins. Run the "Install JavaCV…" plugin and the necessary library files will be downloaded to your Image or Fiji installation. Restart ImageJ/Fiji, and a new options should appear in the Plugins folder called "Ffmpeg Video". ![]() He has kindly allowed me to post the Java code for his plugins here.ĭownload this plugin as a JAR file: Ffmpeg_Importer_Exporter.jarĭirections: To use these plugins, place the JAR file somewhere in the ->plugins folder hierarchy in your ImageJ home directory to enable this functionality. For fluorescence data one normally wouldn't compress primary data using a lossy compressor.Ī complete solution: Ffmpeg FrameReader and Ffmpeg FrameRecorder pluginsįortunately, Stanislav Chizhik (Institute of Solid Chemistry and Mechanochemistry SB RAS, Novosibirsk, Russia) has provided both Ffmpeg-based read and write functionality using JavaCV and Ffmpeg. For Nomarski data this means a major storage hit. A downside is that uncompressed AVIs can be huge (often an order of magnitude larger than movies saved using some codecs). AVI), One approach is to write to uncompressed AVIs, within ImageJ which is supported natively in ImageJ/Fiji, then use your favorite app of choice (Adobe Media Converter, VirtualDub on Windows, or Ffmpeg or wrapper apps that make calls to Ffmpeg on Linux/Mac/Windows) to convert to MP4. ImageJ has major limitations writing to modern video formats such as H264 using the H264 codec and convenient wrappers (.MOV. Instead, it may be easier to use plugins under ImageJ to import QuickTime movies as virtual stacks using Ffmpeg, which will work on 64-bit operating systems and under newer, 64-bit versions of ImageJ. I (Jeff) have successfully tested Mojave with VMWare Fusion. It is possible to use virtualization software to run OS X Mojave or earlier, to retain support for QTJ. Due to its 32-bit architecture, it will not work under 64-bit only operating systems like OS X Catalina. QuickTime for Java (QTJ) has been deprecated for many years by Apple.
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