Thursday, February 28, 2008

importing, format zeiss leica olympus nikon

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…<!--[if supportFields]> XE "Jimi Reader…:Wayne Rasband and Ulf Dittmer (udittmer at mac.com)" <![endif]--> .

La collection de plug-in pour imageJ pour importer:

http://www.uhnresearch.ca/facilities/wcif/imagej/importing_image_files.htm#Import_other

IMPORTING LEICA files:
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.

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. WCIF collection de plug-in.