imageJ import export file format

2. Importing Image Files

ImageJ primarily uses TIFF as the image file format. The menu command “File/Save” will save in TIFF format. The menu command “File/Open” will open TIFF files and import a number of other common file formats (e.g. JPEG, GIF, BMP, PGM, PNG). These natively supported files can also be opened by drag-and-dropping the file on to the ImageJ toolbar. MetaMorph *.STK files can also be opened directly.

Several more file formats can be imported via ImageJ plugins (e.g. Biorad, Noran, Zeiss, Leica). When you subsequently save these files within ImageJ they will no longer be in their native format. Bear this in mind; ensure you do not overwrite original data.

There are further file formats such as PNG, PSD (Photoshop), ICO (Windows icon), PICT, which can be imported via the menu command File/Import/*.PNGJimi Reader… .

2.1 Importing Zeiss LSM files

Files acquired on the Zeiss confocal are can be opened directly (with the “Handle Extra File Types” plugin installed) via the “File/Open” menu command, or by dropping them on the ImageJ toolbar. They can also be imported via the “Zeiss LSM Import Panel” which is activated by the menu command “File/Import/*.LSM”. This plugin has the advantage of being able to access extra image information stored with the LSM file, but it is an extra mouse click.

Images are opened as 8-bit colour images with the “no-palette” pseudocolour (!) from the LSM acquisition software. Each channel is imported as a separate image/stack. Lambda stacks are therefore imported as multiple images, not a single stack. They can be converted to a stack with the menu command: “Image/Stacks/Covert Images to stack”.

Once opened, the file information can be accessed and the z/t/lambda information can be irreversibly stamped in to the images or exported to a text file.

2.2 Importing Zeiss ZVI files

ZVI files can be imported via the menu command « File/Import/*.ZVI« . The files are opened as a single stack with the different channels interleaved. The channels can be separated with the « Plugins/Stacks-Shuffling/DeInterleave » plugin.

2.3 Importing Noran SGI file

Noran movies can be opened in several ways:

File/Import/Noran movie… opens the entire movie as an image stack.
File/Import/Noran Selection…
allows you to specify a range of frames to be opened as a stack.

The Noran SGI plugins are not bundled with the ImageJ package. To receive them, please contact tonyc@uhnresearch.ca or their author, Greg Joss, so he can keep track of users. Greg Joss gjoss AT bio.mq.edu.au is in the Dept of Biology, Macquarie University, Sydney, Australia.

2.4 Importing Biorad PIC files

Biorad PIC files can be now be imported directly via the menu command “File/Open”. Experimental information, calibration, and other useful information can be accessed via Image/Show Info. Biorad PIC files can also be opened by drag-and-dropping the file on to the ImageJ toolbar. The PIC file is opened with the same LUT with which it was saved in the original acquisition software.

2.5 Importing multiple files from folder

Each 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 file. The experimental sequence can be imported to ImageJ via the menu command “File/Import/Image Sequence…”.

Locate the directory, click on the first image in the sequence and OK all dialogs. (You may get a couple of error messages while ImageJ 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.

Selected images that are not the same size can be imported as individual images windows using “File/Import/Selected files to open… ” or as a stack with the “File/Import/Selected files for stack… ”. Unlike the “File/Import/Image Sequence…” function, the images need not be of the same dimensions. If memory is limited, stacks can be opened as Virtual-Stacks with most of the stack remaining on the disk until it is required “File/Import/Disk based stack” .

2.6 Importing Multi-RAW sequence from folder

To form an image, ImageJ needs to know the image dimensions, bit-depth, slice number per file and any extraneous information in the file format (offset and header size). All you really need to tell it is the image dimension in x and y. These values should be obtainable from the software in which the images were acquired. Armed with this information follow these steps:

1. File/Import/Raw…

2. Select experimental directory.

3. Typical values for the dialog box are:

Image type = 16-bit unsigned            (or 8 bit typically)

width and height as determined earlier

offset = 0, number of image = 1, gap = 0, ‘white’ is zero = off

‘Little-endian byte order’ = on, ‘open all files in folder’ = on to open all files in folder.

Non-image files will also be opened and may appear as blank images and need deleting: “Image/Stacks/Delete slice”. The stack will “interleave” the multiple channels you recorded, and can be de-interleaved via “Plugins/Stacks – Shuffling/DeInterleave.

2.7 Importing AVI and MOV files

There are two plugins which can open uncompressed AVIs and some types of MOV file.

For opening (and writing) QuickTime you need a custom installation of QuickTime to include QT for Java (see section 1.3). QuickTime movies are then opened via “File/Import/*.MOV ”.

Uncompressed AVIs can be opened via “File/Import/*.AVI ”.

2.8 Importing Scanalytics IPLab IPL files

IPLab files can be imported directly by ImageJ. File/Import/*.IPL . Allows Windows IPLab files to be opened directly with the “File/Open” menu command, or drag-and-drop.

The spatial calibration should be imported correctly from your IPLab software.

2.9 Importing Leica SP2 LEI series

Leica SP2 experiments are saved as multiple tiff files in a single folder. This can contain many different series acquired during the one experiment. Along with many tiffs, the folder also contains a text description in the *.TXT files and a Leica proprietary file *.LEI.

Double clicking, drag/dropping of « File/Open« ‘ing the *.LEI files should run the Leica TIFF Sequence plugin. Alternatively, run the menu command « File/Import/*.TXT Leica SP2 series » and select the experiment’s TXT file from the open dialog.

A second dialog will open listing the names of the series in the folder. The user can then select those that are to be opened. The appropriate spatial calibration should be read form the txt file and applied to the image. Leica ‘Snapshots’ do not have spatial calibration saved with them. The entry in the TXT file for the series is written to the ‘Notes’ for the image and can be access by the menu command « Image/Show Info…« .

Folders with large numbers of series in could potentially generate a dialog so large that some names are « off screen ». The maximum number of series names per column can be set by running the plugin with the alt-key down.

2.10 Other Import functions

These import plugins import the image data as well as meta-data.

Leica SP- Leica multi-colour images are tiffs. They can be opened as multiple files to a a single stack. Each channel can be imported separately by adding ‘c1′ or c2’ etc. as the import string. Alternatively, they can be all imported to the one stack then separated by de-interleaving them (« Plugins/Stack – shuffling/Deinterleave« ).

Olympus Fluoview – available from http://rsb.info.nih.gov/ij/plugins/ucsd.html. Not bundled with the current download.

Animated GI F – This plugin opens an animated GIF file as an RGB stack. Also opens single GIF images.

File/Import/ICS,IDS Image Cytometry Standard file format from Nico Sturman.

File/Import/*.DV *.DV files generated on DeltaVision system format from Fabrice Cordelieres

File/Import/*.ND *.ND files created with MetaMorph’s ‘Multidimensional acquisition”. From Fabrice Cordelieres

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