LEICA Tiff Sequence Importer

[lechristophe]

Hi all,

I'd like to use the "Leica Tiff Sequence" plugin in a macro. However, I
get an error about spaces that prevent to properly record the plugin
action.

**The following suppose that you know what a Leica SP2 folder output
look like and what the plugin is doing**

What I would like to do is simple : detect the different series in a
folder, and being able to open them sequentially, that is open the first
one, treat it, open the second one, etc...
For the moment I can only open all series in a folder and batch treat
them one after another, using a loop on the images id's. But this is
very memory-hungry, so I would like to be able to open series one at a time.

One a related note, the Leica TIFF importer launches when I try to do a
File>"Import Sequence..." in a folder that contains a .lei file. It is
quite annoying, as sometimes i really want to import a sequence in this
folder, not use this plugin. I think it could be simpler if the plugin
lauched only by calling the plugin directly or by opening .lei file, not
using "Import Sequence..." command. I use MBF Image from Tony Collins +
Leica Tiff Sequence plugin, from Tony Collins also I think, so this
question is really for you Tony ! It's on Mac OSX 10.4.8, ImageJ updated
to 1.38i


Christophe Leterrier

[Tony Collins-4]

> One a related note, the Leica TIFF importer launches when I try to do
a
> File>"Import Sequence..." in a folder that contains a .lei file. It is
> quite annoying, as sometimes i really want to import a sequence in
this
> folder, not use this plugin. I think it could be simpler if the plugin
> lauched only by calling the plugin directly or by opening .lei file,
not
> using "Import Sequence..." command. I use MBF Image from Tony Collins
+
> Leica Tiff Sequence plugin, from Tony Collins also I think, so this
> question is really for you Tony ! It's on Mac OSX 10.4.8, ImageJ
updated
> to 1.38i


That's to do with the *.lei entry in the 'handle extra file types'.

Have you tried the LOCI importer for the SP2 tiff sequences? It's
probably a better way to go.

Cheers,

Tony

[Tony Collins-4]

Sounds like it's not distinguishing between 'channels-first' and
'z-first' acquisition.
I'm not sure of the tag in the txt file that specifies which way the
series was acquired.
Have you a txt file of a 'channels first' series and a 'z first' series?
Our SP5 acquisition software distinguishes the two by 'switching between
frames' (=channels first) and 'switching between stacks'(=z first).
Cheers,

Tony

> -----Original Message-----
> From: Joel Sheffield [mailto:[hidden email]]
> Sent: February 2, 2007 4:14 PM
> To: Tony Collins; ImageJ Interest Group
> Subject: Re: LEICA Tiff Sequence Importer
>
> While we are on this subject, I would like to raise a problem that we
> have been having with the Leica Tiff importers --either the one from
> Tony or the one from the LOCI group.  In a number of experiments, we
> use the Leica "sequential scan" system that allows us to set separate
> settings for each of the channels and to scan them sequentially, so
> that in a z scan series, we have ch1z1, ch2z1, ch1z2 ....etc, but the
> instrument switches laser lines, mirrors, gain and offset between
> each channel, and then proceeds to the next z position. This allows
> us to eliminate crosstalk between channels, and maximize sensitivity.
>
>  Both of the file openers that I have used seem to have a great deal
> of trouble reading these files correctly.  The channels come out
> either mixed together or blank.  Any thoughts?
>
> Date sent:       Fri, 2 Feb 2007 13:23:45 -0500
> Send reply to:   ImageJ Interest Group <[hidden email]>
> From:           Tony Collins <[hidden email]>
> Subject:         Re: LEICA Tiff Sequence Importer
> To:             [hidden email]
>
> > > One a related note, the Leica TIFF importer launches when I try to

do
> > a
> > > File>"Import Sequence..." in a folder that contains a .lei file.
It is
> > > quite annoying, as sometimes i really want to import a sequence in
> > this
> > > folder, not use this plugin. I think it could be simpler if the
plugin
> > > lauched only by calling the plugin directly or by opening .lei
file,
> > not
> > > using "Import Sequence..." command. I use MBF Image from Tony
Collins
> > +
> > > Leica Tiff Sequence plugin, from Tony Collins also I think, so
this

> > > question is really for you Tony ! It's on Mac OSX 10.4.8, ImageJ
> > updated
> > > to 1.38i
> >
> >
> > That's to do with the *.lei entry in the 'handle extra file types'.
> >
> > Have you tried the LOCI importer for the SP2 tiff sequences? It's
> > probably a better way to go.
> >
> > Cheers,
> >
> > Tony
>
>
> --
> Joel B. Sheffield, Ph.D.
> Biology Department, Temple University
> 1900 North 12th Street
> Philadelphia, PA 19122
> [hidden email]
> [phone], fax [phone]
> http://astro.temple.edu/~jbs