Re: problem with Grid/Collection Stitching

Posted by ctrueden on Jun 07, 2016; 6:11pm
URL: http://imagej.273.s1.nabble.com/problem-with-Grid-Collection-Stitching-tp5016603p5016611.html

Hi Michael,

> If you would like a copy of my script send me an email (its long
> enough I did not want to include the whole thing in the email body).

Once really nice way to share such things publicly without polluting email
bodies is to use a gist: https://gist.github.com/

That way, others finding this email thread in the archives later can check
it out.

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - http://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Tue, Jun 7, 2016 at 10:23 AM, Majurski, Michael Paul (Fed) <
[hidden email]> wrote:

> Is the upper left image (0,0) missing? Or is it misplaced?
>
> I have had this happen, but looking in the
> TileConfiguration.registered.txt file shows the (0,0) image has simply been
> put in the wrong place, ending up under another image using an overlay
> blend.
>
> For assembling the TileConfiguration.registered.txt file I use a Matlab
> script to build the stitched image.
> If you would like a copy of my script send me an email (its long enough I
> did not want to include the whole thing in the email body).
>
> ~Michael Majurski
> [hidden email]
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Aryeh Weiss
> Sent: Tuesday, June 07, 2016 10:07 AM
> To: [hidden email]
> Subject: problem with Grid/Collection Stitching
>
> I am not sure if this was posted, so I am resending. My apologies if was
> already posted.
>
>
> I have a directory with files named
> bare60C12minFlat000.tif. bare60C12minFlat001.tif,
> bare60C12minFlat002.tif, ....
>
> So in the plugin I define;
> First file index = 0
> File names for tiles = bare60C12min{iii}.tif
>
> And the plugin does a great job for 120 images, except that the upper
> left corner (0,0) in the fused image is left out, and is black.
>
> The first image in teh ROI list is bare60C12minFlat001.tif . For
> example, here is the first ROI name:
> sp=1; label=0; series=0; C=1; Z=1; T=1; file=bare60C12min001.tif-0
>
> I tried renaming the entire directory to start at 001, but then I get
> the first file as:
> sp=1; label=0; series=0; C=1; Z=1; T=1; file=bare60C12min002.tif-0
>
> and so on.
>
> In there a way to get the plugin to include that first file?
>
> Also, given the TileConfiguration.registered.txt file, is there a way to
> reconstruct the fused image, or should I write a script that reads the
> coordinates, inputs the images, and pastes them appropriately?
>
> Thanks in advance.
>
> --aryeh
>
> --
> Aryeh Weiss
> Faculty of Engineering
> Bar Ilan University
> Ramat Gan 52900 Israel
>
> Ph:  972-3-5317638
> FAX: [phone]
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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