Wright Cell Imaging Facility

 

 

 

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

2006/Feb/24: First version.

2006/Mar/2: Fixed error arising from series with similar names containing spaces; errors arising from images with Gray LUT.

2006/Mar/20: Filenames listed in multiple columns (max number of rows per column can be set by running the plugin with the alt-key down.).

 

 

Source: Leica_TIFF_sequence.java
Installation:

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;
        }
Limitations: Requires ImageJ 1.35m or better.

First release. Based on trial and error dissection of TXT file. Atypical series may throw errors. Please contact me with any errors/fixes.

Description: 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.

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