First images /rows are missing in the stitched images

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First images /rows are missing in the stitched images

Yuekan Jiao-2
Hi

We use Fiji plugin Stitching-Grid/Collection Stitching (or - deprecated
-Stitch Grid of Images / Stitch Sequence of Grid of Images) to stitch
images. Often the first few images of the first row, or the images of the
first few rows and first images of the next row are missing in the stitched
images, eg the first images of an image sequence are missing from the
stitched image.  I tried giving higher tolerance for the plugin in deciding
if an image will be discarded,  for example, I use
regression threshold:  0.1 (if I understand correctly)
max/avg displacement threshold: 5.0

absolute displacement threshold: 7.0

it helps for some image sequences, however for some image sequences the
problem of missing images persists. I am just curious about that the
missing images are the first ones, and if there is way to deal with it.

Thanks

Yuekan Jiao

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Re: First images /rows are missing in the stitched images

Federico Luzzati
I had the same problem, using grid collection.. The plugin version is 2.0.0. I tried to overcome the poblem by adding a dark image to the beginning of the hyperstacks before stitching, but I had a second problem: The command "add" silces by default add after the current image and the "alt" key apparently does not work with Hyperstacks.
Please help!


Federico

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Re: First images /rows are missing in the stitched images

Stephan Preibisch
Hi,

this can be caused by two things. Either there is a shift in z so that it does set it one plane back, or it might be caused because of the subpixel accuracy. Try disabling that.

It seems quite some people have this problem, so I could add an option to disregard any translation in z?

Nice greetings,
Stephan

On May 30, 2013, at 2:28 , Federico Luzzati wrote:

> I had the same problem, using grid collection.. The plugin version is 2.0.0. I tried to overcome the poblem by adding a dark image to the beginning of the hyperstacks before stitching, but I had a second problem: The command "add" silces by default add after the current image and the "alt" key apparently does not work with Hyperstacks.
> Please help!
>
>
> Federico
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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Re: First images /rows are missing in the stitched images

Rasband, Wayne (NIH/NIMH) [E]
In reply to this post by Federico Luzzati
On May 30, 2013, at 2:28 AM, Federico Luzzati wrote:

> I had the same problem, using grid collection.. The plugin version is 2.0.0. I tried to overcome the poblem by adding a dark image to the beginning of the hyperstacks before stitching, but I had a second problem: The command "add" silces by default add after the current image and the "alt" key apparently does not work with Hyperstacks.
> Please help!

In the ImageJ 1.47r daily build, there is a "Prepend" option in the Image>Stacks>Add Slice dialog box that allows you to add a channel, slice or frame to the beginning of a hyperstack.

-wayne

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Re: First images /rows are missing in the stitched images

L'assegnista
Hi guys, Thank you all.
Stephan: I resolved the problem of the dark planes by unchecking the
subpixel accuracy. Now all the images of the stacks are displeyed in the
fused image.
Wayne: I did'nt tried yet but I'll do soon.

Best regards

Federico Luzzati


Il 02.06.2013 05:34 Rasband, Wayne (NIH/NIMH) [E] ha scritto:

> On May 30, 2013, at 2:28 AM, Federico Luzzati wrote:
>
>> I had the same problem, using grid collection.. The plugin version
>> is 2.0.0. I tried to overcome the poblem by adding a dark image to the
>> beginning of the hyperstacks before stitching, but I had a second
>> problem: The command "add" silces by default add after the current
>> image and the "alt" key apparently does not work with Hyperstacks.
>> Please help!
>
> In the ImageJ 1.47r daily build, there is a "Prepend" option in the
> Image>Stacks>Add Slice dialog box that allows you to add a channel,
> slice or frame to the beginning of a hyperstack.
>
> -wayne
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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Federico Luzzati, PhD
Researcher
Dept. Life Sciences and Systems Biology
University of Turin
Via Accademia Albertina, 13
10123 Torino
Neuroscience Institute Cavalieri Ottolenghi (NICO)
Regione Gonzole, 10
10043 Orbassano (Torino)
ITALY
tel. +39-011670-4683/ -6631

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Re: First images /rows are missing in the stitched images

Yuekan Jiao-2
In reply to this post by Stephan Preibisch
Hi Stephan,

Thank you for looking into it. My image sequences are just 2D images, and
disabling subpixel does not avoid the problem for me.

I am willing to supply some example images if you like.

Yuekan


On Sat, Jun 1, 2013 at 9:20 AM, Stephan Preibisch <[hidden email]>wrote:

> Hi,
>
> this can be caused by two things. Either there is a shift in z so that it
> does set it one plane back, or it might be caused because of the subpixel
> accuracy. Try disabling that.
>
> It seems quite some people have this problem, so I could add an option to
> disregard any translation in z?
>
> Nice greetings,
> Stephan
>
> On May 30, 2013, at 2:28 , Federico Luzzati wrote:
>
> > I had the same problem, using grid collection.. The plugin version is
> 2.0.0. I tried to overcome the poblem by adding a dark image to the
> beginning of the hyperstacks before stitching, but I had a second problem:
> The command "add" silces by default add after the current image and the
> "alt" key apparently does not work with Hyperstacks.
> > Please help!
> >
> >
> > Federico
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Re: First images /rows are missing in the stitched images

Stephan Preibisch
Hi Yuekan,

that would be very helpful!

Thanks a lot,
Stephan

On Jun 3, 2013, at 13:42 , Yuekan Jiao wrote:

> Hi Stephan,
>
> Thank you for looking into it. My image sequences are just 2D images, and
> disabling subpixel does not avoid the problem for me.
>
> I am willing to supply some example images if you like.
>
> Yuekan
>
>
> On Sat, Jun 1, 2013 at 9:20 AM, Stephan Preibisch <[hidden email]>wrote:
>
>> Hi,
>>
>> this can be caused by two things. Either there is a shift in z so that it
>> does set it one plane back, or it might be caused because of the subpixel
>> accuracy. Try disabling that.
>>
>> It seems quite some people have this problem, so I could add an option to
>> disregard any translation in z?
>>
>> Nice greetings,
>> Stephan
>>
>> On May 30, 2013, at 2:28 , Federico Luzzati wrote:
>>
>>> I had the same problem, using grid collection.. The plugin version is
>> 2.0.0. I tried to overcome the poblem by adding a dark image to the
>> beginning of the hyperstacks before stitching, but I had a second problem:
>> The command "add" silces by default add after the current image and the
>> "alt" key apparently does not work with Hyperstacks.
>>> Please help!
>>>
>>>
>>> Federico
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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