Re: FIJI 2D stitching in a macro

Posted by Stephan Preibisch on Nov 16, 2010; 9:16am
URL: http://imagej.273.s1.nabble.com/Advice-petition-on-learning-java-programming-tp3686421p3686427.html

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/