leica SP2 tiff sequence – ressources

formats:

  • tiff
  • volume tiff
  • raw
  • avi

———————————–

plug-in imageJ

This plugin opens multi-TIFF series acquired with Leica SP2 confocal.

Run the plugin; select the TXT file associated with the TIFF series and select the series to be opened. This information is then passed to the native « Import Sequence » function.

Optional ability to split the channels.

The plugin should apply the spatial calibration found in the TXT file.

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]–> .

exemple pour Zeiss LSM:

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.

plug-in download:

http://rsbweb.nih.gov/ij/plugins/leica-tiff.html

2006/02/16:First version
2006/03/02:Fixed error arising from series with similar names containing spaces; errors arising from images with Gray LUT.
2006/03/20:Filenames listed in multiple columns (max number of rows per column can be set by running the plugin with the alt-key down.).

—–author

Author: Tony Collins (tonyc at uhnresearch.ca)
Wright Cell Imaging Facility, Toronto, Canada

http://www.uhnresearch.ca/facilities/wcif/software/Plugins/LeicaTIFF.html

Save to plugins folder; compile and run plugin.
The compiled version is bundled with latest WCIF ImageJ bundle along with modified HandleExtraFileTypes.class (courtesy of Greg Jefferis) to allow double-clicking of the *.LEI file to open the sequence.

Code for HandleExtraFileTypes.java from Greg:

//  Leica SP confocal .lei file handler
        if (name.endsWith(".lei")) {
            int dotIndex = name.lastIndexOf(".");
            if (dotIndex>=0)
                name = name.substring(0, dotIndex);
            path = directory+name+".txt";
            File f = new File(path);
            if(!f.exists()){
                IJ.error("Cannot find the Leica information file: "+path);
                return null;
            }
            IJ.runPlugIn("Leica_TIFF_sequence", path);
            width = IMAGE_OPENED;
            return null;
        }

———————-Huygens Software reads and writes

The Huygens Software reads and writes (among other → File Formats) TIFF series with Leica style numbering if there are more channels (different wavelength), slices or frames (in a Time Series) than in a simple Numbered Tiff series.

An image of four slices and two frames is named with Leica style numbering as follows:

c_t00_z000.tif
c_t00_z001.tif
c_t00_z002.tif
c_t00_z003.tif
c_t01_z000.tif
c_t01_z001.tif
c_t01_z002.tif
c_t01_z003.tif

And an image sTCh of four slices, three frames and two channels:

sTCh_t00_z000_ch00.tif
sTCh_t00_z000_ch01.tif
sTCh_t00_z001_ch00.tif
sTCh_t00_z001_ch01.tif
sTCh_t00_z002_ch00.tif
sTCh_t00_z002_ch01.tif
sTCh_t00_z003_ch00.tif
sTCh_t00_z003_ch01.tif
sTCh_t01_z000_ch00.tif
sTCh_t01_z000_ch01.tif
sTCh_t01_z001_ch00.tif
sTCh_t01_z001_ch01.tif
sTCh_t01_z002_ch00.tif
sTCh_t01_z002_ch01.tif
sTCh_t01_z003_ch00.tif
sTCh_t01_z003_ch01.tif
sTCh_t02_z000_ch00.tif
sTCh_t02_z000_ch01.tif
sTCh_t02_z001_ch00.tif
sTCh_t02_z001_ch01.tif
sTCh_t02_z002_ch00.tif
sTCh_t02_z002_ch01.tif
sTCh_t02_z003_ch00.tif
sTCh_t02_z003_ch01.tif
------------

-----------------------quelques ressources des centres
http://www-ijpb.versailles.inra.fr/fr/lcc/fichiers/equip-sp2.htm
http://www-ijpb.versailles.inra.fr/fr/lcc/fichiers/pdf/instruction-utilisation-SP2.pdf

http://www.itg.uiuc.edu/ms/equipment/microscopes/lscm.htm
leica LCS lite

http://microscopy.unc.edu/How-to/leicasp2/default-viewing.html

http://ijm2.ijm.jussieu.fr/imagerie/fichiers

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