http://imagej.273.s1.nabble.com/problem-with-Grid-Collection-Stitching-tp5016603p5016715.html
I finally had a chance to try this, and it works. I found that when I
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>
> On Fri, Jun 10, 2016 at 7:41 AM, Aryeh Weiss <
[hidden email]> wrote:
>
>> 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
>>>>