stitching RGB images

[Aryeh Weiss]

I have 70 color TIFF images which I am stitching, using the excellent
grid/collection stitching plugin.

It does a great job, and I see that it processes all of the colors.
However, it then produces an 8-bit color image, instead of the expected
RGB image. I can actually see all three images being created, but then
they are combined into a single 8-bit image.

Is there a way to have it create an RGB fused image? Or, can I get at
the three images that it creates before merging them into an 8-but color
image?

--aryeh

--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Peter Haub]

Hi Aryeh,

you can register the images on one channel and creating a
TileConfiguration. This TileConfiguration can then be used to stitch the
channels separately.

The channel images should have identical size and should be aligned to
each other.
If the channel images are not to big, you can combine the R/G/B channels
with the standard ImageJ function( Image / Color / Merge channels ..).

The image size limit is given by your OS (32bit or 64bit), your RAM,
Java JRE (32bit or 64bit) or/and the limited array size in Java (2^31).

Regards,

Peter

On 28.06.2016 23:20, Aryeh Weiss wrote:

> I have 70 color TIFF images which I am stitching, using the excellent
> grid/collection stitching plugin.
>
> It does a great job, and I see that it processes all of the colors.
> However, it then produces an 8-bit color image, instead of the
> expected RGB image. I can actually see all three images being created,
> but then they are combined into a single 8-bit image.
>
> Is there a way to have it create an RGB fused image? Or, can I get at
> the three images that it creates before merging them into an 8-but
> color image?
>
> --aryeh
>

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

Hi, the plugin uses Composite Images that instead of the wasteful and inflexible RGB images (using 32 bits per pixel where it is only 24 bit that are used for 3 channels  and even only 16bit for 2 channels).

You can always convert it later back to RGB if you like: Image > Type > RGB color.

Hope this helps,
Stephan
---

Dr. Stephan Preibisch
Group Leader

Berlin Institute of Medical Systems Biology of the MDC
Building 89, 1.08b

email: [hidden email]<mailto:[hidden email]>
web: http://www.preibisch.net/<http://fly.mpi-cbg.de/preibisch>

On 28 Jun 2016, at 17:20, Aryeh Weiss <[hidden email]<mailto:[hidden email]>> wrote:

I have 70 color TIFF images which I am stitching, using the excellent grid/collection stitching plugin.

It does a great job, and I see that it processes all of the colors. However, it then produces an 8-bit color image, instead of the expected RGB image. I can actually see all three images being created, but then they are combined into a single 8-bit image.

Is there a way to have it create an RGB fused image? Or, can I get at the three images that it creates before merging them into an 8-but color image?

--aryeh

--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html


--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Aryeh Weiss]

Thanks to Stephen and Peter for their replies.

On 29/06/2016 6:34 AM, [hidden email] wrote:
> Hi, the plugin uses Composite Images that instead of the wasteful and
> inflexible RGB images (using 32 bits per pixel where it is only 24 bit
> that are used for 3 channels  and even only 16bit for 2 channels).
>
It happens that the NIS Elements software that generates the images
conveniently names them tile_x{xxx}_y{yyy}.tif, so I was ableto feed
them directly into the stitching program. However, it creates RGB, and
does not know from composite, so it would be convenient for the
stitching program, which anyway is creating all three channels, to
produce a composite output.
However, if it will not do that, I can write a macro that will convert
the input images to composite. It is just a step I hoped I could skip.
> You can always convert it later back to RGB if you like: Image > Type
> > RGB color.
>
I feed the output into the color deconvolution plugin (thank you
Gabriel), so I will see if that ill take composite images or wants RGB.

> Hope this helps,
Indeed it did. Thanks again.
--aryeh

> Stephan
> ---
>
> Dr. Stephan Preibisch
> Group Leader
>
> Berlin Institute of Medical Systems Biology of the MDC
> Building 89, 1.08b
>
> email:[hidden email]
> <mailto:[hidden email]>
> web: http://www.preibisch.net/ <http://fly.mpi-cbg.de/preibisch>
>
>> On 28 Jun 2016, at 17:20, Aryeh Weiss <[hidden email]
>> <mailto:[hidden email]>> wrote:
>>
>> I have 70 color TIFF images which I am stitching, using the excellent
>> grid/collection stitching plugin.
>>
>> It does a great job, and I see that it processes all of the colors.
>> However, it then produces an 8-bit color image, instead of the
>> expected RGB image. I can actually see all three images being
>> created, but then they are combined into a single 8-bit image.
>>
>> Is there a way to have it create an RGB fused image? Or, can I get at
>> the three images that it creates before merging them into an 8-but
>> color image?
>>
>> --aryeh
>>
>> --
>> Aryeh Weiss
>> Faculty of Engineering
>> Bar Ilan University
>> Ramat Gan 52900 Israel
>>
>> Ph:  972-3-5317638
>> FAX: [phone]
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]


--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Peter Haub]

Hi Stephan,

when I remember correctly from my work with Composite Images the
alignment is done on every channel. This leads to stitching artifacts
when working with RGB images because the registration is different for
the different channels.

Peter

On 29.06.2016 12:34, [hidden email] wrote:

> Hi, the plugin uses Composite Images that instead of the wasteful and inflexible RGB images (using 32 bits per pixel where it is only 24 bit that are used for 3 channels  and even only 16bit for 2 channels).
>
> You can always convert it later back to RGB if you like: Image > Type > RGB color.
>
> Hope this helps,
> Stephan
> ---
>
> Dr. Stephan Preibisch
> Group Leader
>
> Berlin Institute of Medical Systems Biology of the MDC
> Building 89, 1.08b
>
> email: [hidden email]<mailto:[hidden email]>
> web: http://www.preibisch.net/<http://fly.mpi-cbg.de/preibisch>
>
> On 28 Jun 2016, at 17:20, Aryeh Weiss <[hidden email]<mailto:[hidden email]>> wrote:
>
> I have 70 color TIFF images which I am stitching, using the excellent grid/collection stitching plugin.
>
> It does a great job, and I see that it processes all of the colors. However, it then produces an 8-bit color image, instead of the expected RGB image. I can actually see all three images being created, but then they are combined into a single 8-bit image.
>
> Is there a way to have it create an RGB fused image? Or, can I get at the three images that it creates before merging them into an 8-but color image?
>
> --aryeh
>
> --
> Aryeh Weiss
> Faculty of Engineering
> Bar Ilan University
> Ramat Gan 52900 Israel
>
> Ph:  972-3-5317638
> FAX: [phone]
>
> --
> 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

Hi,

no, not if it is a Composite image, it then computes the average intensity of all channels and uses this for computing the alignment. Only if you provide each channel as separate image (e.g. one TIFF each), then, this will happen.

All the best,
Stephan

---

Dr. Stephan Preibisch
Group Leader

Berlin Institute of Medical Systems Biology of the MDC
Building 89, 1.08b

email: [hidden email]<mailto:[hidden email]>
web: http://www.preibisch.net/<http://fly.mpi-cbg.de/preibisch>

On 29 Jun 2016, at 07:27, Peter Haub <[hidden email]<mailto:[hidden email]>> wrote:

Hi Stephan,

when I remember correctly from my work with Composite Images the alignment is done on every channel. This leads to stitching artifacts when working with RGB images because the registration is different for the different channels.

Peter

On 29.06.2016 12:34, [hidden email]<mailto:[hidden email]> wrote:
Hi, the plugin uses Composite Images that instead of the wasteful and inflexible RGB images (using 32 bits per pixel where it is only 24 bit that are used for 3 channels  and even only 16bit for 2 channels).

You can always convert it later back to RGB if you like: Image > Type > RGB color.

Hope this helps,
Stephan
---

Dr. Stephan Preibisch
Group Leader

Berlin Institute of Medical Systems Biology of the MDC
Building 89, 1.08b

email: [hidden email]<mailto:[hidden email]><mailto:[hidden email]>
web: http://www.preibisch.net/<http://fly.mpi-cbg.de/preibisch><http://www.preibisch.net/%3Chttp://fly.mpi-cbg.de/preibisch%3E>

On 28 Jun 2016, at 17:20, Aryeh Weiss <[hidden email]<mailto:[hidden email]><mailto:[hidden email]>> wrote:

I have 70 color TIFF images which I am stitching, using the excellent grid/collection stitching plugin.

It does a great job, and I see that it processes all of the colors. However, it then produces an 8-bit color image, instead of the expected RGB image. I can actually see all three images being created, but then they are combined into a single 8-bit image.

Is there a way to have it create an RGB fused image? Or, can I get at the three images that it creates before merging them into an 8-but color image?

--aryeh

--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html


--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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