http://imagej.273.s1.nabble.com/problem-with-Grid-Collection-Stitching-tp5016603p5017324.html
left tile not appearing in the fusion occurs starting at 90 tiles. For
displayed. If I do 10x9 of these tiles, the upper left tile will not be
displayed. But if I do 8x11, then it will be displayed. This behavior is
> Thank you for this reply.
>
> On 13/06/2016 9:50 PM, Yuekan Jiao wrote:
>> My method requires Grid/Collection type "Filename defined position", i.e.
>> you will need to rename your images to the format of
>> "image_Y{yyy}_X{xxx}.tif". Then add a black row Y000 if your first row is
>> Y001. Stitch all the images including Y000.
>>
>> I explored plugin Grid/Collection stitching a bit for the re-assembling.
>> Open the registration file "TileConfiguration.registered.txt", delete the
>> lines of the added black row Y000. Run plugin Grid/Collection stitching
>> again, this time select type "Positions from file". Input
>> "TileConfiguration.registered.txt"
>> as "Layout file", uncheck "Compute overlap", you will get all the
>> images in
>> the stitched image.
>> Yuekan
>
> I finally had a chance to try this, and it works. I found that when I
> assembled the image this way, it was complete.
> This means that the problem was only in the display of the fusion, but
> the TileConfiguration.registered.txt file included the missing tile
> correctly, without the need for a black row.
>
> This is exactly what I needed to know.
>
> Best regards
> --aryeh
>
>
>
>>
>>
>> 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
>>>>>
>