README for SER_Reader

Version: 0.1 (2017-02-01, 11:00 mmohn)

Copyright

(c) 2017 Michael Mohn, Ulm University

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.

Features

Special features for image stacks larger than the computer's memory:

• limit range of slices to read, e.g. only 100th to 500th slice
• read large image stacks with increment > 1, e.g. every 2nd image

Features for image stacks:

• recording time is copied to the slice metadata of the image slice. (Date and time in the time zone of the computer that runs ImageJ). Unfortunately, the precision is only 1 second.

Installation

In order to use this reader plugin via the ImageJ open dialog or via drag & drop, the plugin should be installed in the Input-Output folder (ImageJ/plugins/Input-Output) and the HandleExtraFileTypes plugin has to be modified, too. I added the following lines to the "HandleExtraFileTypes.java" file in the Input-Output folder:

	// TIA ser files (SER_Reader)
	// --------------------------
	if (name.endsWith(".ser")) {
        return tryPlugIn("SER_Reader", path);
	}

Please remember to compile both the SER_Reader plugin and the HandleExtraFileTypes plugin.

Known issues:

• calibration is read once for 1st slice, assuming same calibration for all slices. Only width, height and image type will be checked for other slices.
• 1D data is not supported (spectra)!
• reader doesn't check whether file is too large for memory