Multiple Image sequence open commands in a macro

[Guenter Giese]

Dear list members,
 
I would like to improve a macro by which I open several image sequences from
one directory.
 
This macro contains multiple command lines like:
 
run("Image Sequence...", "+((open)+  number=stack_size starting=1
increment=1 scale=100 file=r00 sort use)");
run("Image Sequence...", "+((open)+  number=stack_size starting=1
increment=1 scale=100 file=r01 sort use)");
run("Image Sequence...", "+((open)+  number=stack_size starting=1
increment=1 scale=100 file=r02 sort use)");
 
when I run the macro with, e.g. eight run("Image Sequence...",  lines , the
File.open dialog is opened eight times.
 
Since, ***any** image file in the directory can be chosen (double-clicked)
during each dialog (the macro handles the file selection), it should be
sufficient to choose a file only once (i.e. by the first dialog only, or by
a previous dialog) .
 
Such a file name can be queried from the user by:
path = File.openDialog("Select a File");
I tried to pass this "path" to the run("Image Sequence...", ) lines, but
this did not work yet.
 
How can I pass the path and filename to all the run("Image Sequence...",)
instances to have all the other file sequences opened automatically?
 
Best,
 
Guenter
---------------------------------------------------------------------
Dr. Guenter Giese
Light Microscopy Facility Manager
Dept. of Biomedical Optics
MPI fuer Medizinische Forschung Jahnstr. 29
D-69120 Heidelberg, Germany
Phone [phone] (Fax: -325)
e-mail: [hidden email]
 

[Wayne Rasband]

> I would like to improve a macro by which I open several image
> sequences from one directory.
>
> This macro contains multiple command lines like:
>
> run("Image Sequence...", "+((open)+  number=stack_size starting=1
> increment=1 scale=100 file=r00 sort use)");
> run("Image Sequence...", "+((open)+  number=stack_size starting=1
> increment=1 scale=100 file=r01 sort use)");
> run("Image Sequence...", "+((open)+  number=stack_size starting=1
> increment=1 scale=100 file=r02 sort use)");
>
> when I run the macro with, e.g. eight run("Image Sequence...",
> lines, the File.open dialog is opened eight times.
>
> Since, ***any** image file in the directory can be chosen
> (double-clicked) during each dialog (the macro handles the file
> selection), it should be sufficient to choose a file only once (i.e.  
> by
> the firs dialog only, or by a previous dialog) .
>
> Such a file name can be queried from the user by:
> path = File.openDialog("Select a File");
> I tried to pass this "path" to the run("Image Sequence...", )
> lines but this did not work yet.
>
> How can I pass the path and filename to all the run("Image  
> Sequence...",)
> instances to have all the other file sequences opened automatically?

Use code something like this:

   path = "/Users/wayne/Downloads/stack/";
   run("Image Sequence...", "open=&path file=r00 sort use");
   run("Image Sequence...", "open=&path file=r01 sort use");
   run("Image Sequence...", "open=&path file=r02 sort use");

The "number=stack_size", "starting=1", "increment=1" and "scale=100"  
options can be omitted (the default values are used).

The "&path" notation for passing variables like 'path' requires ImageJ  
1.43 or later. With earlier versions you have to use string  
concatenation:

   run("Image Sequence...", "open=["+path+"] file=r00 sort use");
   run("Image Sequence...", "open=["+path+"] file=r01 sort use");
   run("Image Sequence...", "open=["+path+"] file=r02 sort use");

The brackets ("[" and "]") are required if the path can contain spaces.

-wayne

[Bernhard Reber]

hello all,

I intend to try using imageJ together with Leica DFC cameras hooked up to various microscopes.

Any chance at all to get an image displayed be it on the Mac or PC/XP partition on my iMac ?

What extension or plugins are necessary to use Leicas DFC cameras (DFC320/DFC420) together with imageJ ?

Many thanks for any advice or hint !

Bernie

[Kai Toellner]

Bernie,

The "Twain Scan" plugin works for us with the DFC350 FX camera on a Windows XP computer.

Kai

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Bernhard Reber
Sent: 16 December 2009 18:52
To: [hidden email]
Subject: Use of Leica DFC320/420 cameras w/imagej

hello all,

I intend to try using imageJ together with Leica DFC cameras hooked up to various microscopes.

Any chance at all to get an image displayed be it on the Mac or PC/XP partition on my iMac ?

What extension or plugins are necessary to use Leicas DFC cameras (DFC320/DFC420) together with imageJ ?

Many thanks for any advice or hint !

Bernie

[Thorsen, Anders]

Hi

In the software (Leica FireCam) that follows these cameras for the Mac, you can select another program to auto open the pictures you acquire in Leica Firecam. Choose pictures to auto-open in ImageJ. Works very well.

Leica Firecam you can download free from Leica´s website.


anders



On 16 Dec 2009, at 19:51, Bernhard Reber wrote:

> hello all,
>
> I intend to try using imageJ together with Leica DFC cameras hooked up to various microscopes.
>
> Any chance at all to get an image displayed be it on the Mac or PC/XP partition on my iMac ?
>
> What extension or plugins are necessary to use Leicas DFC cameras (DFC320/DFC420) together with imageJ ?
>
> Many thanks for any advice or hint !
>
> Bernie