I may have found the cause of my problem stitching stacks with 5 planes...

[Gelman, Laurent]

Hi everybody,


Following my last e-mail (see below), I looked at http://fiji.sc/Image_Stitching#Problems.2C_known_issues_and_solutions (thanks to Pariksheet Nanda) and it is stated that Z-stacks should have at least 3 planes. I tested different numbers (adding empty planes to my stacks), and actually any number equal to or above 8 seem fine. I guess this is because it is now possible to merge 7 channels...??

If this is the answer, then I would find nice, provided that image properties are set correctly, if the plugin could not convert Z-planes into channels. It does happen to make Z-stacks with less than 8 planes...



Many thanks in advance for your help,



Best regards (and have a nice week-end),



Laurent.



From: Gelman, Laurent
Sent: 05 July 2013 13:28
To: '[hidden email]'
Subject: Stitching of Z-stacks converts Z planes into color channels. Is this normal ?

Hi everybody,

I try to stitch 3D stacks (5 planes, 1 channel) with the Grid/Collection stitching plugin but the displayed fused image is a multi-channel one with 1 plane, with new number of channels = number of Z-planes. Obviously Stitching in Z is also wrong.
Does that mean that I can't stitch Z-stacks this way?

Thanks for your help,

Best regards,

Laurent.

___________________________
Laurent Gelman, PhD
Friedrich Miescher Institut
Facility for Advanced Imaging and Microscopy
Head of Light Microscopy
WRO 1066.2.16
Maulbeerstrasse 66
CH-4058 Basel
[phone]
[phone]


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[Stephan Preibisch]

Hi Laurent,

I suspect that something may go wrong when loading the images. Do you use
TIFFs?

Nice greetings,
Stephan

> Hi everybody,
>
>
> Following my last e-mail (see below), I looked at
> http://fiji.sc/Image_Stitching#Problems.2C_known_issues_and_solutions
> (thanks to Pariksheet Nanda) and it is stated that Z-stacks should have at
> least 3 planes. I tested different numbers (adding empty planes to my
> stacks), and actually any number equal to or above 8 seem fine. I guess
> this is because it is now possible to merge 7 channels...??
>
> If this is the answer, then I would find nice, provided that image
> properties are set correctly, if the plugin could not convert Z-planes
> into channels. It does happen to make Z-stacks with less than 8 planes...
>
>
>
> Many thanks in advance for your help,
>
>
>
> Best regards (and have a nice week-end),
>
>
>
> Laurent.
>
>
>
> From: Gelman, Laurent
> Sent: 05 July 2013 13:28
> To: '[hidden email]'
> Subject: Stitching of Z-stacks converts Z planes into color channels. Is
> this normal ?
>
> Hi everybody,
>
> I try to stitch 3D stacks (5 planes, 1 channel) with the Grid/Collection
> stitching plugin but the displayed fused image is a multi-channel one with
> 1 plane, with new number of channels = number of Z-planes. Obviously
> Stitching in Z is also wrong.
> Does that mean that I can't stitch Z-stacks this way?
>
> Thanks for your help,
>
> Best regards,
>
> Laurent.
>
> ___________________________
> Laurent Gelman, PhD
> Friedrich Miescher Institut
> Facility for Advanced Imaging and Microscopy
> Head of Light Microscopy
> WRO 1066.2.16
> Maulbeerstrasse 66
> CH-4058 Basel
> [phone]
> [phone]
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

... [show rest of quote]

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[Pariksheet Nanda]

On Fri, Jul 5, 2013 at 5:08 PM, Stephan Preibisch <[hidden email]> wrote:
On Fri, Jul 5, 2013 at 10:16 AM, Gelman, Laurent <[hidden email]> wrote:
>> I tested different numbers (adding empty planes to my
>> stacks), and actually any number equal to or above 8 seem fine. I guess
>> this is because it is now possible to merge 7 channels...??
>>
>> If this is the answer, then I would find nice, provided that image
>> properties are set correctly, if the plugin could not convert Z-planes
>> into channels. It does happen to make Z-stacks with less than 8 planes...
>>
--snip--
> I suspect that something may go wrong when loading the images. Do you use
> TIFFs?
>

Hi Stephan,

What's happening is using "Image output"="Fuse and display", shows the
Z slices as channels if there are less than (8) Z slices.
When using more than (8) slices, the Z appears correctly.
In both cases, the data is written correctly when using "Image
output"="Write to disk" - it saves the filenames with z1, z2, etc. and
importing the data with LOCI Bioformats populates creates Z stacks.

I was able to reproduce this problem with today's continuous build of
FIJI, Stitching_-2.0.0-SNAPSHOT and Bioformats-4.4.9.
Data type = ome.tif files, 1 timepoint, 1 channel, 3 z slices, 3x3
grid, created by Micro-Manager 1.4.15.
You can download the data (11 MB) here:
https://drive.google.com/file/d/0By6i416w_DypOTctbG1vZTNkLWc/edit?usp=sharing
The settings I use to open the data in FIJI are:
1) Open "Grid/Collection Stitching" plugin with:
"Positions from File"
"Defined by image metadata"
2) Set "Browse for Multi_series file" to first image.
3) Uncheck "Compute overlap ..."
4) Set "Increase overlap %" to 0
5) Check "Invert Y coordinates"


Best wishes,

>> Laurent.

> Stephan

Pariksheet

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