In particular, you should avoid exporting data using the Bio-Formats Exporter because the files it writes might not be readable later by release versions of Bio-Formats or other OME-compliant tools.įiji ships release versions of Bio-Formats. The daily builds are not yet released and should be considered beta in quality. Run the macro from the command line e.g.:.Click “Create” to pop up the Script Editor, edit as desired, then save the macro as a.Use the Macro Recorder to record the line of macro code that runs Bio-Formats that way you want.You can invoke Bio-Formats from the command line using the ImageJ Launcher: Calling Bio-Formats from the command line In the case of Fiji, we recommend that you do not use this method of update, but instead use the ImageJ Updater. The Update Bio-Formats Plugins command will check online for updates to the Bio-Formats Plugins. You can also drag and drop files onto the shortcut window to open them quickly using the Bio-Formats Importer plugin. The Bio-Formats Plugins Shortcut Window is a small window with a quick-launch button for each plugin. In addition, you can see a list of available helper libraries used by Bio-Formats on the Libraries tab. You can also configure any specific options for each format-for example, for QuickTime, you can toggle between Apple’s QTJava library or Bio-Formats’s built-in support. You can see a list of supported file formats on the Formats tab, toggle each format on or off (which is useful, for example, if your file is being detected as the wrong format), and toggle whether each format bypasses the importer options dialog using the “Windowless” checkbox. The Bio-Formats Plugins Configuration dialog is a useful way to configure the behavior of each file format. It can also be used standalone to split a stack across channels, focal planes or time points. The Stack Slicer plugin is a helper plugin used by the Bio-Formats Importer. The Bio-Formats Macro Extensions plugin prints out the available commands to the ImageJ log window, along with instructions for using them. The Bio-Formats plugins come with a set of macro extensions to enable additional functionality from macros. If you find that you always use the same import settings, you may wish to use the windowless importer to save time. The Bio-Formats Windowless Importer is a version of the Bio-Formats Importer plugin that runs with the last used settings to avoid popping up any additional dialogs beyond the file chooser. It is likely to be less robust than working with files on disk, so when possible we recommend downloading your data to disk and using the regular Bio-Formats Importer instead. The Bio-Formats Remote Importer is a plugin for importing data from a remote URL. On the other hand, the file extensions *.tf2, *.tf8, and *.btf are automatically associated with the 64-bit BigTIFF format, which can store much bigger data.
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