Re: FIJI 2D stitching in a macro

Posted by Jacqueline Ross on Nov 17, 2010; 5:20am
URL: http://imagej.273.s1.nabble.com/Advice-petition-on-learning-java-programming-tp3686421p3686428.html

Hi Stephan,

I have updated my Fiji version and still got the same results
unfortunately.

Thanks.

Kind regards,

Jacqui

Jacqueline Ross

Biomedical Imaging Microscopist
Biomedical Imaging Research Unit
School of Medical Sciences
Faculty of Medical & Health Sciences
The University of Auckland
Private Bag 92019
Auckland, NEW ZEALAND

Tel: [phone] Ext 87438
Fax: [phone]

http://www.fmhs.auckland.ac.nz/sms/biru/


-----Original Message-----
From: Stephan Preibisch [mailto:[hidden email]]
Sent: Tuesday, 16 November 2010 10:16 p.m.
To: Jacqui Ross; 'ImageJ Interest Group'
Subject: RE: FIJI 2D stitching in a macro

Hi,

when did you record this macro? Very recently, there was a bug fixed in
the
Macro recording of the 2d-stitching where the field names were slightly
modified, it seems you still have the old field names...might that be
the
case? Then simply re-recording should solve the problem.

Nice greetings,
Stephan

> -----Original Message-----
> From: Jacqui Ross [mailto:[hidden email]]
> Sent: Dienstag, 16. November 2010 05:02
> To: ImageJ Interest Group
> Cc: Stephan Preibisch
> Subject: RE: FIJI 2D stitching in a macro
>
> Hi Stephan,
>
> Thanks for your fast reply. At the moment, all I can do is get the
> first
> 2 images to fuse and that image is saved into my "Tiled" folder.
> However, that image then needs to be merged with the file called
> "bottom" but I get an error then as shown in the attached document.
>
> In case the attachment doesn't come through, the error states as

below:

>
> Numeric value expected in run() function Dialog box title: "Stitching
> of 2D Images"
> Key: "fusion alpha"
> Value or variable name" "Linear Blending"
>
>
> The macro I have recorded is as below;
>
> open("C:\\Documents and Settings\\jros013\\Desktop\\Copy of
> test\\top\\top001.tif"); open("C:\\Documents and
> Settings\\jros013\\Desktop\\Copy of test\\middle\\middle001.tif");
> open("C:\\Documents and Settings\\jros013\\Desktop\\Copy of
> test\\bottom\\bottom001.tif"); run("2D Stitching", "first=top001.tif
> _use_channel_for_first=[Red, Green and Blue] second=middle001.tif
> use_channel_for_second=[Red, Green and Blue] use how=5 create
> _fusion=[Linear Blending] fusion=1.50
> fused=Fused_top001.tif_middle001.tif compute_overlap x=0 y=0");

run("2D

> Stitching", "first=Fused_top001.tif_middle001.tif
> use_channel_for_first=[Red, Green and Blue] second=bottom001.tif
> use_channel_for_second=[Red, Green and Blue] use how=5 create
> fusion=[Linear Blending] fusion=1.50
> fused=Fused_top001.tif_middle001.tif compute_overlap x=0 y=0");
> saveAs("Tiff", "C:\\Documents and Settings\\jros013\\Desktop\\Copy of
> test\\Tiled\\Fused_top001.tif_middle001.tif");
> close();
>
> I will also need to change the naming and make it generic so that it
> sequentially goes through all of the images in the folders in order

and
> creates a tiled image from each one. I then want to create the AVI
from

> those tiled images.
>
> If you can assist with working out what is causing the error, it would
> be much appreciated.
>
> Kind regards,
>
> Jacqui
>
> Jacqueline Ross
>
> Biomedical Imaging Microscopist
> Biomedical Imaging Research Unit
> School of Medical Sciences
> Faculty of Medical & Health Sciences
> The University of Auckland
> Private Bag 92019
> Auckland, NEW ZEALAND
>
> Tel: [phone] Ext 87438
> Fax: [phone]
>
> http://www.fmhs.auckland.ac.nz/sms/biru/
>
>
> -----Original Message-----
> From: Stephan Preibisch [mailto:[hidden email]]
> Sent: Tuesday, 16 November 2010 2:03 p.m.
> To: 'ImageJ Interest Group'
> Cc: Jacqui Ross
> Subject: RE: FIJI 2D stitching in a macro
>
> Hi,
>
> you should be able to record a macro that stores what allowed you to
> merge it for one timepoint. In the ideal case you simple make a loop
> over the 1000 images and it should be fine. At which point are you
> stuck?
>
> Nice greetings,
> Stephan
>
> > -----Original Message-----
> > From: ImageJ Interest Group [mailto:[hidden email]] On Behalf

Of

> > Jacqui Ross
> > Sent: Montag, 15. November 2010 21:53
> > To: [hidden email]
> > Subject: FIJI 2D stitching in a macro
> >
> > Dear All,
> >
> > One of our users has acquired time-lapse data on a Nikon BioStation
> > that she now wants to merge into a movie. She has acquired 3 images
> at
> > each time point, which can be merged together nicely using the 2D
> > Stitch plugin.
> >
> > However, there are over 1000 sets of images ("top", "middle" and
> > "bottom") to be merged.
> >
> > Is anyone able to let me know how I can put this into a macro? We
> have
> > 3
> > data sets of tiff files sequentially named in 3 individual folders,
> > top, middle and bottom. The tiling is not straightforward in that it
> > is
> like
> > a zigzag rather than a rectangle. However, the 2D plugin did merge
> the
> > 3
> > images very well so if we can automate the procedure and obtain the
> > merged tiff files for each time point, we can then easily build the
> > AVI.
> >
> > I have looked at the batch processing options but I haven't figured
> out
> > how to select the correct images.
> >
> > Thanks in advance for any assistance.
> >
> > Kind regards,
> >
> > Jacqui
> >
> > Jacqueline Ross
> >
> > Biomedical Imaging Microscopist
> > Biomedical Imaging Research Unit
> > School of Medical Sciences
> > Faculty of Medical & Health Sciences
> > The University of Auckland
> > Private Bag 92019
> > Auckland, NEW ZEALAND
> >
> > Tel: [phone] Ext 87438
> > Fax: [phone]
> >
> > http://www.fmhs.auckland.ac.nz/sms/biru/