Do I need to recalibrate holder images after instrument reset/restart?

[KerstinGruender]

Hi,
this is the first of likely a few more questions about PfE as I'm getting to know the features and working with it. Starting with a short one:
I have loaded and calibrated an image of our own holders into stage.exe to be able to do mosaic imaging (BSE and SEI). Works well. Yet to fogure out the best way to stitch the bmp images, but that's another topic.

Question: After a full reset of the EPMA (JEOL JXA 8230), all the way down to the main power switch at the wall, i.e. full restart including stage initialize - does this throw out these holder image calibrations? And what about any PictureSnap images I had loaded before the reset, and position files? Will they all be 'off' now? I guess I could go and test this, but we're pretty booked and on the clock with paying external users, but I want to know whether I need to make time for this or not.

Cheers,
Kerstin

[Probeman]

I have loaded and calibrated an image of our own holders into stage.exe to be able to do mosaic imaging (BSE and SEI). Works well. Yet to fogure out the best way to stitch the bmp images, but that's another topic.

When you say "into stage.exe" I assume you mean the StageMap window?  As shown here:

https://smf.probesoftware.com/index.php?topic=417.msg6797#msg6797

Actually, now that I re-read your post I see you probably mean the Stage.exe Digitize Mosaic Image Acquisition window... which utilizes the same WMF files as the StageMap window.

Question: After a full reset of the EPMA (JEOL JXA 8230), all the way down to the main power switch at the wall, i.e. full restart including stage initialize - does this throw out these holder image calibrations? And what about any PictureSnap images I had loaded before the reset, and position files? Will they all be 'off' now? I guess I could go and test this, but we're pretty booked and on the clock with paying external users, but I want to know whether I need to make time for this or not.

This is an excellent question. The answer is: it depends!

If you are concerned about the accuracy of the stage calibration on an image that covers your entire sample holder (as in the example in the link above), the reproducibility of the stage self-test after a re-boot is probably fine. Probably within 10 um or better, depending on the age of the stage mechanicals.

But if the image is a high magnification image, then of course the image calibration may not be good enough after a stage self-test.

I would definitely run a test or two. I know on my Cameca SX100 the stage reproducibility after a stage re-boot was excellent but then that stage utilized optical encoders.

See here for some tips on image calibration of the StageMap images:

https://smf.probesoftware.com/index.php?topic=1581.msg12195#msg12195

Also here is a link to a topic that discusses using Probe Image or Surfer to mosaic the sub images after acquisition:

https://smf.probesoftware.com/index.php?topic=324.0

[KerstinGruender]

Thank you! Given that the image is not super high magnification in order to fit into the application, then it will probably fine. I will keep it in mind if users have high res images loaded into PictureSnap however, and we had to do a reset in which case it might pay to check.

And yes, the calibration was done via the StageMap window, then utilized the same image in Stage.exe Digitize Mosaic Image Acquisition window 

In regards to mosaic stitching, I have been able to stitch the grd files with Surfer following the instructions in your linked forum post, but this then only gave me options of false colour/relief image using the information in the grd files? Not stitching the actual bmp grayscale BSE images that were acquired and are inside the same mosaic folder. Have not worked out yet whether Surfer can do this or what else to use. I didn't do enough overlap to do it in ImageJ/Fiji, but that may work otherwise.

Kerstin

[Probeman]

In regards to mosaic stitching, I have been able to stitch the grd files with Surfer following the instructions in your linked forum post, but this then only gave me options of false colour/relief image using the information in the grd files? Not stitching the actual bmp grayscale BSE images that were acquired and are inside the same mosaic folder. Have not worked out yet whether Surfer can do this or what else to use. I didn't do enough overlap to do it in ImageJ/Fiji, but that may work otherwise.

You can mosaic your GRD files in Surfer, and then export as BMP or JPEG or whatever. You might want to check out some of the Surfer webinars from Golden Software:

https://www.goldensoftware.com/support/webinars/

If you acquire PrbImg/TIF files in Probe Image, they can be mosaiced together using the Advanced | Concatenate menu:

https://smf.probesoftware.com/index.php?topic=132.msg542#msg542