Saving and Exporting

Cookbook Topics
Introduction and Installation
Annotating Images
Color Image Processing
Image Intensity Processing
Importing Image Files
Particle Analysis
Saving and Exporting
Stack-slice Manipulations

Image formats

Save as1.png
Save as2.png
The “File/Save” (hotkey: S) menu command will save the image as a TIF file. Other formats are available (see menu image on the right) and can be accessed by “File/Save As...”. When the “Save as” dialog is opened, Fiji will enter the image window’s name, plus the appropriate file suffix, as the “File Name".

Animated GIF… Choosing this option from the "Save as" menu saves a stack as an animated GIF. It is only compatible on RGB or 8 bit images. A more suitable option would be saving as GIF, where the only limitation is that any RGB color stacks must be converted to 8 bit color.

Uncompressed AVI files are exported via “File/Save as…/AVI…” . The frame rate and compression option of the exported AVI movie is selected in the resulting window. Frame rate can be between 0.1 and 100 frames per second (fps). The compression may be in JPEG, PNG, or uncompressed. Though uncompressed files are large, they should be playable on any PC/Mac without decoder issues.

Flash MX will import uncompressed AVI files. The frame-rate will then be determined by Flash, not the AVI movie file.

Other options for saving and exporting image files are shown in the Fiji Save As menu. Their procedures are all straightforward.

Image sequences

Image Sequence... This option saves each slice in a stack as a separate TIF file. You will be presented with the option to either name the images numerically or with the slice labels.

Non-image formats

Selection... After drawing an ROI onto an image, the selection's coordinates can be saved using this option. Once the ROI is deselected, it can be restored at any time in the same location by opening the saved ROI.

XY Coordinates... This option is similar to "Save as/Selection...", but this choice saves the coordinates of the selection in a text file with two columns for X and Y coordinates.

Results... This uses the information in an active results window and exports it into a text file.


Files may also be exported to many file types using Plugins ▶ Bio-Formats ▶ Bio-Formats Exporter. As of this writing, the supported file types are:

  • Animated PNG
  • AVI
  • Encapsulated PostScript (EPS, EPSI)
  • Image Cytometry Standard (IDS, ICS)
  • Java source code
  • JPEG
  • JPEG-2000
  • QuickTime
  • TIFF

See the Export column of the Bio-Formats list of supported formats for an up-to-date list of formats which can be exported.