Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocalI ran into this problem several years ago, with a Leica sp1. At the
time, Benjamin Matthieu wrote up a set of routines that import the
files, allowing you to select which ones you want. The set has not
been made publically available because they are still somewhat crude.
However, I would be happy to share them.
My file structure involves a file name of the form:
r5 6-8-04_Series002_t00_z002_ch00.tif
in which the channels switch at each z level.
Mattieu's plugin has an option called : time proj. This reads the
selected channel, and then for each time point, reads all of the z
positions into a temporary stack, and then does a Max projection of
the stack. That projection is then added to a new stack that grows
with each time point. The end result is a single stack in which each
image is the max projection of the images of a "single" time point.
The process is quite slow, since it involves reading and writing a
large number of images.
A major problem with these routines is that they do not insert the
calibration data into the images. You do that by clicking on
"parameters", and entering the data manually into the properties
fields.
Also, when you select a file, you have to reclick on it to cancel.
Nevertheless, I find them quicker than the LOCI routines, and they
are sensitive to sequential scan records.
Joel
> Search the CONFOCAL archive at
>
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal>
> Hi all,
>
> Can anyone tell me whats the easiest way to import a multiple channel
> with z stacks time-lapse sequence into imageJ? We used a Leica sp2 so
> the file type is Leica .lei
>
> thanks,
>
> Matt Pearson.
--
Joel B. Sheffield, Ph.D.
Biology Department, Temple University
1900 North 12th Street
Philadelphia, PA 19122
[hidden email]
(215) 204 8839, fax (215) 204 0486
http://astro.temple.edu/~jbs
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