All you really need to tell it is the image dimension in x and y. To form an image, Fiji needs to know the image dimensions, bit-depth, slice number per file and any extraneous information in the file format (offset and header size). If memory is limited, stacks can be opened as Virtual-Stacks with most of the stack remaining on the disk until it is required. Then you can put those images into a stack by Image › Stacks › Images to stack Unlike the File › Import › Image Sequence function, the images don’t need to be the same dimensions. Selected images that are not the same size can be imported as individual images windows using File › Import and select each individual image you want imported into Fiji. (You may get a couple of error messages while Fiji tries to open any non-image files in the experimental directory.) The stack will “interleave” the multiple channels you recorded, and can be de-interleaved via Plugins › Stacks - Shuffling › Deinterleave Locate the directory, click on the first image in the sequence and OK all dialogs. The experimental sequence can be imported to Fiji via the menu command File › Import › Image Sequence. Multiple files from a folderĮach time point of an experiment acquired with software such as Perkin Elmer’s UltraVIEW or Scion Image’s time lapse macro is saved by the acquisition software as a single TIF. Once opened, the file information can be accessed and the information can be irreversibly stamped into the images or exported. They can be converted to a stack with the menu command: Image › Stacks › Images to stack. Lambda stacks are therefore imported as multiple images, not a single stack. Each channel is imported as a separate image/stack. Images are opened as 8-bit color images with the “no-palette” pseudo color from the LSM acquisition software. Once you select LSM the panel will appear. The LSM Toolbox is activated by the menu command File › Import › LSM. The LSM panel plugin duplicates the Zeiss LSM file import function of the LOCI Bio-Format Importer, but will also extensively catalogue the LSM metadata. Select this command if you need to change the settings for importing an image. With this option, Fiji uses the settings that were previously used for Bio-Formats, so it skips all dialog boxes at the beginning. But it is a limited feature it is more robust to download the file and then use the regular Bio-Formats instead. For this selection, the image doesn’t have to be saved onto your computer or a disk. There are several different Bio-Formats commands for importing data into Fiji: In these cases a second dialog will list the images in the ‘database’ prompting you to select which to open. Some image file formats are more akin to databases rather than images (e.g. If Bio-Formats is used, you will be prompted with a big dialog and your preferences remembered.ĭrag and dropping an image file to the Fiji toolbar will effectively open the file the same as the File › Open command. See the list of supported file formats on the Bio-Formats website for the complete list (135 as of this writing). They can be accessed directly via the menu command File › Import › Bio-Formats or indirectly via the File › Open menu command which will use the Bio-Formats plugin if needed. This will import and export a wide number of file formats along with their important metadata. Many more file formats can be imported via Fiji plugins. Files can be also dragged and dropped to the toolbar to open them. JPEG, GIF, BMP, PGM, PNG) as well as those detailed below. The menu command File › Open will open TIFF files and import a number of other common file formats (e.g. ![]() ![]() The menu command File › Save will save in TIFF format. Built-in formatsįiji primarily uses TIFF as the image file format. Most of the commands listed, particularly Fiji extensions, are also available (via ImageJ’s HandleExtraFileTypes feature) simply by using the File › Open… menu item. If you’d like to help, check out the how to help guide! The File › Import submenu The content of this page has not been vetted since shifting away from MediaWiki.
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