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. Tagged Image File Format (TIFF) (*.tif, *.tiff, *.tf2, *.tf8, *.btf)įor OME-TIFF and TIFF formats, the file extensions *.tif and *.tiff are associated with the standard 32-bit TIFF, which has a 4GB size limit.Image Cytometry Standard (*.ids, *.ics).Encausupated PostScript (*.eps, *.epsi).It can save to the open OME-TIFF file format, as well as several movie formats (e.g., QuickTime, AVI) and graphics formats (e.g., PNG, JPEG). The Bio-Formats Exporter is a plugin for exporting data to disk. The Bio-Formats Importer plugin may be able to import such TIFFs successfully. For example, by default Fiji uses some built-in logic to open TIFF files, but this logic may fail with certain TIFFs. However, for certain file formats, you may wish to explicitly activate the Bio-Formats Importer to override the default behavior of Fiji. Often, you will not need to worry about this plugin to import your data, because Bio-Formats is largely integrated with the File › Open command of Fiji. It will also extract and set basic metadata values such as spatial calibration if they are available in the file. It can open many dozens of proprietary life sciences formats, and standardize their acquisition metadata into a common OME data model. The Bio-Formats Importer is a plugin for reading data into Fiji. See especially the Using Bio-Formats page for detailed instructions. See the Bio-Formats website for additional information about Bio-Formats in general. You will find them all under the “Bio-Formats” submenu of Plugins. What follows is a brief overview of the available plugins. See LOCI’s Bio-Formats site for a historical narrative of the project. Import data from many life sciences file formats, and export to several open formats.
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