Posted by
Majurski, Michael Paul (Fed) on
Jun 07, 2016; 3:09pm
URL: http://imagej.273.s1.nabble.com/problem-with-Grid-Collection-Stitching-tp5016603p5016604.html
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: 972-3-7384051
--
ImageJ mailing list:
http://imagej.nih.gov/ij/list.html--
ImageJ mailing list:
http://imagej.nih.gov/ij/list.html