Posted by
Aryeh Weiss on
Jun 10, 2016; 2:41pm
URL: http://imagej.273.s1.nabble.com/problem-with-Grid-Collection-Stitching-tp5016603p5016623.html
Thank you to Michael and Yuekan for their replies to my inquiry.
I have been traveling, but when I have a chance I will try to translate
Michael's MATLAB script to an ImageJ script.
I can add that I just tried to reassemble a 12 image grid which was
named in similar way (tile_001, tile_002, ... tile_012), and
which happened to be listed by row (the 120 image grid that showed this
problem was ordered by column).
It worked without leaving anything out.
On 07/06/2016 8:57 PM, Yuekan Jiao wrote:
> Hi,
>
> This problem was discussed a while ago, it looks that plugin
> Grid/Collection Stitching still has it. What I do is to add a black row
> before the first row. After stitching all the images including the added
> black row, re-assemble the images without the added black row based on the
> registration file TileConfiguration.registered.txt. Either a script or
> plugin Grid/Collection Stitching itself (just my impression) will do the
> job. I use my own script but have not tried plugin Grid/Collection
> Stitching for the re-assembling.
Can you post your script for reassembling the montage?
> Yuekan
>
> On Tue, Jun 7, 2016 at 8:23 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.
My TileConfiguration.registered.txt shows the first image as being at
(0.0, 0.0), which I assume makes sense because everything else moves
relative to that image.
>> 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).
As noted above, I will try to adapt that script to ImageJ and I will
try it.
>> ~Michael Majurski
>>
[hidden email]
Best regards
--aryeh
>> -----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>>
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>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>
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> ImageJ mailing list:
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--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel
Ph: 972-3-5317638
FAX: 972-3-7384051
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