the substring "ch00" contained in LEICA SP2 files of the first channel of an the image series) Sequence Options > File name contains : enter a substring unique for a single channel, e.g.Opening with the standard ImageJ configuration (the harder way) now arrange on the monitor to view side by side.(to split multicolor stacks into individual channels:) Plugins > Stacks - Shuffling > DeinterleaveĬhoose the channel of interest (#.) from each series, bring to front File > import *.TXT Leica SP2 series (choose *.txt file, usually the second file of the list).Download the Tony Collins compilation of ImageJ and Plugins from here:.Opening with the Tony Collins compilation of ImageJ / plugins Leica SP2 series).Ĭaveat: I highly recommend to work with a copy of your data, not with the original! The Leica file system does not like any changes at all). Initially collated from the ImageJ home page to help the Laboratory of Molecular Signaling in Babraham Institute (UK), I developed it further at the Wright Cell Imaging Facility (TWRI, Canada) here it was released as WCIF ImageJ.
Wcif imagej software manual#
Stored as single channel / single z plane series, like, e.g. The ImageJ for Microscopy bundle and accompanying manual was developed to manage this wide-ranging array of plugins.
It creates a folder named "fancy" (your whole experiment name) and in this folder, it stores: When you store such an experiment, you store this whole experiment giving it a name (e.g. Lets suggest you recorded two stacks with three channels each (series1, series2, series3). Such an Experiment can contain not only one scan, but several stacks, time series etc. LEICA LCS software stores data in "Experiments".
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