How to capture stitched/montage images

[Kline, David D.]

Greetings,

I am curious on how I can capture a montage of images and have them stitched together in micromanager. We used to be able to do this in the Slide Explorer Plugin in MM 1.3, but on our 64 bit Win 7, MM 1.4 system this ability is no longer functional.

Any help or ideas would be appreciated.
Thanks,

Dave

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[Thorn, Kurt]

What do you mean, "is no longer functional"?  I was using the slide
explorer plugin last night on the latest MM build on 64bit Win 7.

Kurt

On 11/1/2011 8:02 AM, Kline, David D. wrote:

> Greetings,
>
> I am curious on how I can capture a montage of images and have them stitched together in micromanager. We used to be able to do this in the Slide Explorer Plugin in MM 1.3, but on our 64 bit Win 7, MM 1.4 system this ability is no longer functional.
>
> Any help or ideas would be appreciated.
> Thanks,
>
> Dave
>
> ------------------------------------------------------------------------------
> RSA® Conference 2012
> Save$700 by Nov 18
> Register now
> http://p.sf.net/sfu/rsa-sfdev2dev1
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[Kline, David D.]

Sorry- yes, the Slide Explorer is functional, but the ability to save the images is not (unless I am missing something). That is what I intended to say, my apologies.  

-----Original Message-----
From: Kurt Thorn [mailto:[hidden email]]
Sent: Tuesday, November 01, 2011 11:43 AM
To: [hidden email]
Subject: Re: [micro-manager-general] How to capture stitched/montage images

What do you mean, "is no longer functional"?  I was using the slide explorer plugin last night on the latest MM build on 64bit Win 7.

Kurt

On 11/1/2011 8:02 AM, Kline, David D. wrote:

> Greetings,
>
> I am curious on how I can capture a montage of images and have them stitched together in micromanager. We used to be able to do this in the Slide Explorer Plugin in MM 1.3, but on our 64 bit Win 7, MM 1.4 system this ability is no longer functional.
>
> Any help or ideas would be appreciated.
> Thanks,
>
> Dave
>
> ----------------------------------------------------------------------
> --------
> RSA® Conference 2012
> Save$700 by Nov 18
> Register now
> http://p.sf.net/sfu/rsa-sfdev2dev1
> _______________________________________________
> micro-manager-general mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/micro-manager-general

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[Brice B.]

Kline, David D. wrote

Greetings,

I am curious on how I can capture a montage of images and have them stitched together in micromanager. We used to be able to do this in the Slide Explorer Plugin in MM 1.3, but on our 64 bit Win 7, MM 1.4 system this ability is no longer functional.

Hello,
I currently use a plugin to integrate with stitching ImageJ: http://pacific.mpi-cbg.de/wiki/index.php/Stitching_2D/3D .

The fact that this feature is no longer on the slide explore is a blessing in disguise because it allowed us to treat the blanc-field before picking up the images.

It is very easy to make a macro that does the job and the stitching plugin allows you to place the images according to their coordinates and the job is done faster without errors.

Best,
Brice

[Kline, David D.]

Thanks Brice!

How do you capture the coordinates you wish to later stitch together? Do you use the tile creator plugin?

I am coming from Neurolucida which allows us to draw a ROI around the region at 4 X we want stitched together, and then capture at a higher magnification. This ensures there is enough overlap for the stitching.

Many thanks for your help.

Dave  

-----Original Message-----
From: Brice B. [mailto:[hidden email]]
Sent: Tuesday, November 08, 2011 3:32 AM
To: [hidden email]
Subject: Re: [micro-manager-general] How to capture stitched/montage images


Kline, David D. wrote:
>
> Greetings,
>
> I am curious on how I can capture a montage of images and have them
> stitched together in micromanager. We used to be able to do this in
> the Slide Explorer Plugin in MM 1.3, but on our 64 bit Win 7, MM 1.4
> system this ability is no longer functional.
>
>

Hello,
I currently use a plugin to integrate with stitching ImageJ:
http://pacific.mpi-cbg.de/wiki/index.php/Stitching_2D/3D .

The fact that this feature is no longer on the slide explore is a blessing in disguise because it allowed us to treat the blanc-field before picking up the images.

It is very easy to make a macro that does the job and the stitching plugin allows you to place the images according to their coordinates and the job is done faster without errors.

Best,
Brice



-----
Neurogénétique comportementale
INCIA
UMR 5287 CNRS-Université Bordeaux1

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[Brice B.]

Hi David,

Kline, David D. wrote

How do you capture the coordinates you wish to later stitch together? Do you use the tile creator plugin?

I am coming from Neurolucida which allows us to draw a ROI around the region at 4 X we want stitched together, and then capture at a higher magnification. This ensures there is enough overlap for the stitching.

You have several options:
-You can use the coordinates in the metadata of your images (and XPositionUm YPositionUm) taken with slideexplorer. You have a preview of your area but you will have to make a macro to retrieve the coordinates and deduct your grid. In addition, we failed to use an objective for the preview and another one to take the samples (this should be possible ...).

-You can use the "Create Grid" in "Tools -> XYList ...". There is no preview but you can choose your area, your objective (especially the pixel size ...), and your overlap (it is in microns and u will calculate the percentage value ...).
You can use the "2D/3D Stitching" plugin. You fill "Directory" normally and "file names" with a command like this: "/ 2-Pos_ {xxx} {yyy} _ / img_000000000__000.tif".

In command line it looks something like this:
"run (" Stitch Grid of Images "," grid_size_x grid_size_y = 3 = 3 overlap = 0 directory = C: / AcquisitionData/quinine_1 file_name = / 2-Pos_ {xxx} {yyy} _ / img_000000000__000.tif rgb_order = rgb = output_file_name TileConfiguration.txt start_x start_y = 0 = 6 = 1 start_ channels_for_registration = [Red, Green and Blue] fusion_method = [Linear Blending] fusion_alpha regression_threshold = 1.50 = 0.30 max / avg_displacement_threshold absolute_displacement_threshold = 2.50 = 3.50 ");"

-We have developed several small scripts to initialize the stage, to preview the entire sample with objective 2.5x, and demarcate a zone on the preview to be taken into 10x objective and reconstituted with stitching and white correction.
There would be some adjustments to make it work with your hardware. The code is not yet very clean.


Best regards
Brice