Author Topic: Automated Mosaic Imaging (using Stage.exe)  (Read 16047 times)

Probeman

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Re: Automated Mosaic Imaging (using Stage.exe)
« Reply #30 on: September 27, 2016, 11:22:35 am »
I recently ran a BSE stage beam mosaic on one of my standard blocks, first with zero overlap between the sub-images and second, with a 1% overlap between the sub images.  Here is the mosaic dialog in the Stage application:



And this is the digitized image centers after clicking the Digitize Mosaic button:



The reduced size mosaics are attached below (remember you need to be logged in to see attachments), but here is a closeup on a couple of standards that have two sub images overlapping:



Even though "ground mode" was selected in the Beam dialog of PeakSight there is still some change in BSE signal that apparently cannot be stabilized.  If anyone has any suggestions on to to force the BSE detector to not change its intensity response when performing multiple beam scan acquisitions, please let me know!

The beam scan calibration utilized in this mosaic is described in this topic, though the sub image magnifications used in the mosaics were around 150x to 180x, while the lowest beam scan calibration magnification defined was 334x:

http://probesoftware.com/smf/index.php?topic=396.0
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John Donovan

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Re: Automated Mosaic Imaging (using Stage.exe)
« Reply #31 on: June 27, 2017, 10:22:50 pm »
I made some improvements to the mosaic feature in Stage based on suggestions from Paul Carpenter:



1. Add mouse cursor stage coordinates to the window caption.

2. A new checkbox to "lock" the mosaic grid to the current position. Useful when wanting to move to each corner to focus the z stage,

3. A new button to reset all four corner Z positions all to the current Z stage position value.

4. Display of the number of mosaic "sub-images" to be digitized/acquired.

Please update your PFE, try it out, and let me know what else you need for your mosaic acquisition needs.
john
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John Donovan

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Re: Automated Mosaic Imaging (using Stage.exe)
« Reply #32 on: June 30, 2017, 09:28:05 am »
The latest release of Probe for EPMA has further improvements to the Stage.exe mosaic feature, including display of the number of columns and rows of the grid as seen here:



Note that if you utilize the sub image toggle feature in the Stage Mosaic window to turn off sub images that are not of interest (areas of epoxy, etc.), you cannot use the ImageJ stitch plugin and will need to use the Grid | Mosaic menu in Surfer to mosaic your GRD files.  Well, there appears to be a feature for that plugin to define the row, column order of the sub images, but that would be extra work.
john
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glennpoirier

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Re: Automated Mosaic Imaging (using Stage.exe)
« Reply #33 on: July 10, 2017, 05:43:06 am »
Hi all,
I'm having a brain fart, how do I get Surfer to output a bitmap image of my mosaic GRD file? I'm sure I've done it before but I can't remember exactly how I did it.Thanks

Probeman

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Re: Automated Mosaic Imaging (using Stage.exe)
« Reply #34 on: July 10, 2017, 08:24:31 am »
Hi all,
I'm having a brain fart, how do I get Surfer to output a bitmap image of my mosaic GRD file? I'm sure I've done it before but I can't remember exactly how I did it.Thanks

Hi Glenn,
Use the File | Export menu. Then select the image type (.jpg. .png, etc.), then select the pixel resolution.
john
« Last Edit: July 10, 2017, 11:47:55 am by Probeman »
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glennpoirier

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Re: Automated Mosaic Imaging (using Stage.exe)
« Reply #35 on: July 12, 2017, 11:56:18 am »
Hi John,
When I open the GRD image in Surfer I don't get an Export command in the File window. Am i missing something else?

Thanks

Glenn

Probeman

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Re: Automated Mosaic Imaging (using Stage.exe)
« Reply #36 on: July 12, 2017, 12:02:25 pm »
Hi John,
When I open the GRD image in Surfer I don't get an Export command in the File window. Am i missing something else?

Thanks

Glenn

Hi Glenn,
Ah, OK.

Yes, you do not need to open the mosaic GRD file in Surfer. Instead once you "mosaic" the GRD files, you need to use the Map | New | Image Map menu, and then select "mosaiced" GRD file you want to display.  Then you should be able to use the Export menu to create a JPG, BMP, etc. file.
john
« Last Edit: July 12, 2017, 01:03:49 pm by Probeman »
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glennpoirier

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Re: Automated Mosaic Imaging (using Stage.exe)
« Reply #37 on: July 14, 2017, 12:25:19 pm »
Aha!
Thanks I know there was missing step.
Cheers
Glenn

Probeman

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Re: Automated Mosaic Imaging (using Stage.exe)
« Reply #38 on: September 18, 2017, 04:44:15 pm »
I've been working with a geology student, Marisa Acosta, using the Stage app to acquire automated mosaic images in CL and BSE.

Here is a CL scan of a petrographic thin section originally scanned at 400x (512 x 512 pixel sub images) which comes to over 20,000 pixels wide!   The final image was mosaiced in Surfer using the Grid | Mosaic menu.

The attached image below is subsampled at much lower resolution, but you get the idea...

Paul Carpenter and I are still working to improve the mosaic feature in Stage, but it produces very high resolution large area maps with very little effort.
john
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Probeman

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Re: Automated Mosaic Imaging (using Stage.exe)
« Reply #39 on: October 03, 2017, 12:45:48 pm »
We ran some additional thin sections using the mosaic feature in Stage, for both BSE and CL and are now using these as "base maps" for planning our trace element analyses.  The original mosaics are over 1300 sub images and over 20K pixels wide.

The images attached below (please login to see attachments) are rescaled to 2048 pixels wide.
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BenjaminWade

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Re: Automated Mosaic Imaging (using Stage.exe)
« Reply #40 on: October 03, 2017, 10:34:01 pm »
Hey John
That is a really nifty feature. I admit I don't utilise the Stage mapping feature yet but definitely one to add to the list.
I have a quick questions off-topic about your CL detector/settings. What is the sample you are mapping here that is luminescing. I have the Panchromatic CL that comes with the Cameca SXFive, but have found it to be very insensitive. Unless I am trying to CL benitoite...which is never.
Can I ask what kind of beam settings, frame time, Cat PM, offset/gain settings you are using on your CL signal? Do you have the standard Cameca CL or are you using one purchased separately?

Cheers

Probeman

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Re: Automated Mosaic Imaging (using Stage.exe)
« Reply #41 on: October 04, 2017, 10:01:03 am »
Hey John
That is a really nifty feature. I admit I don't utilise the Stage mapping feature yet but definitely one to add to the list.
I have a quick questions off-topic about your CL detector/settings. What is the sample you are mapping here that is luminescing. I have the Panchromatic CL that comes with the Cameca SXFive, but have found it to be very insensitive. Unless I am trying to CL benitoite...which is never.
Can I ask what kind of beam settings, frame time, Cat PM, offset/gain settings you are using on your CL signal? Do you have the standard Cameca CL or are you using one purchased separately?

Cheers

Hi Ben,
Nothing special, just the Cameca PMT as shown here:

http://probesoftware.com/smf/index.php?topic=883.0

Note the above link shows the fiber coupled spectrometer in the acquisition position, but we can just slide things to the right to get the PMT in place.

I do tend to run the PMT a bit high, around 900 or 1000.
john
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John Donovan

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Re: Automated Mosaic Imaging (using Stage.exe)
« Reply #42 on: November 19, 2017, 05:58:48 pm »
We added a checkbox control to specify filament standby in the Stage.exe app, perhaps for when one is acquiring a large number of mosaic scans and the run will go into the night.
john
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Mike Matthews

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Re: Automated Mosaic Imaging (using Stage.exe)
« Reply #43 on: January 24, 2018, 10:54:02 am »
Hi John,

I've been trying to mosaic one of my standards blocks and I'm obviously doing something wrong at some point. I've calibrated the beam scan conditions at the kV and mag and input them into the .ini file, stored the image co-ords, and successfully acquired the images. I load them into Probe Image (Is there a way to load all the images at once? I tried shift+click and curl+click in the open dialog and can only select one image at a time). When I select the mosaic command from the Concatenate menu PI tells me the image isn't registered (many many times!) and fails to build the concatenated image. Do you know what I'm missing out?

John Donovan

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Re: Automated Mosaic Imaging (using Stage.exe)
« Reply #44 on: January 24, 2018, 11:50:19 am »
Hi Mike,
We've been planning to add a "Load All Images From Folder" and a "Load All Selected Images From Folder" menus but haven't gotten around to it.   But because loading the images one by one is tedious it makes more sense to use the Grid | Mosaic menu in Surfer to load all your images (as .GRD files) and mosaic them in Surfer.  That's how I've been doing Stage mosaics (see above posts for examples) for some time now and it works great though it takes a few minutes if you have many images.

On the beam scan calibrations for imaging in Probe for EPMA remember that you don't need to edit the Probewin.ini by hand any longer.  You can use the 3 point calibration method using beam scan images from Probe for EPMA and a stage scan from Probe Image and calibrate them in CalcImage using the new three point calibration method.  If you use this CalcImage beam scan calibration method, the calibrations can be saved automatically to the Probewin.ini file. See here for more details:

http://probesoftware.com/smf/index.php?topic=396.0

As for the images in Probe Image not being calibrated, that is very strange.  Remember though, Probe Image does *not* utilize the beam scan calibrations from the Probewin.ini file. It has it's own beam scan calibration which is accessed from the Setup | Probe Image Setup menu as seen here:



Note that you can certainly just enter the values from the Probe for EPMA calibration into this dialog.
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