ImageJ: working with image series - a few hints

LEICA LCS files

LEICA LCS software stores data in "Experiments". Such an Experiment can contain not only one scan, but several stacks, time series etc. Lets suggest you recorded two stacks with three channels each (series1, series2, series3) . When you store such an experiment, you store this whole experiment giving it a name (e.g. "fancy".)

What Leica Software does:

It creates a folder named "fancy" (your whole experiment name) and in this folder, it stores:

• two files (fancy.lei and fancy.txt) containing different parameters
• single channel, single plane tiff files named as follows:
  experiment_series_channel_plane.tif
  (e.g. fancy_series1_ch000_z00.tif)
• the channel number and z slice number are incremented in the following files, e. g.
  fancy_series1_ch0001_z00.tif
  fancy_series1_ch0000_z01.tif
  fancy_series1_ch0001_z01.tif
  fancy_series1_ch0001_z00.tif

Open a z stack series

Stored as single channel / single z plane series, like, e.g. Leica SP2 series).

Caveat: 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).

Opening with the Tony Collins compilation of ImageJ / plugins

• Download the Tony Collins compilation of ImageJ and Plugins from here:
  http://lightmicro.mpimf-heidelberg.mpg.de/facil/staff/upload/computing/imagej/WCIF_ImageJ_setup_060228_v135q.exe
• Install the ImageJ package
• File > import *.TXT Leica SP2 series (choose *.txt file, usually the second file of the list)
• choose stacks of interest
  (to split multicolor stacks into individual channels:) Plugins > Stacks - Shuffling > Deinterleave
  choose the channel of interest (#...) from each series, bring to front
• now arrange on the monitor to view side by side

Opening with the standard ImageJ configuration (the harder way)

• File > Open image sequence
• Choose the first image of the series
• Do either:
  • Sequence Options > File name contains : enter a substring unique for a single channel, e.g. the substring "ch00" contained in LEICA SP2 files of the first channel of an the image series)
• Or do - more cumbersome, but may help in some cases:
  • choose number of starting image (important: the starting "image" is actually the first file, which may be a non-image file, e.g. *.lei or *.txt file)
  • choose increment (increment usually resembles the number of channels in your image sequence)

Maximum projection of image stacks

• Duplicate your original stack (for a projection from a subset of images: copy the respective images of interest into another directory and load this subset into ImageJ; duplicate it)
• Choose Image > Stacks > Z project