Automated Mosaic Imaging (using Stage.exe)

[Probeman]

OK, I've found them and loaded them into Surfer to generate a mosaic .GRD which I've opened in Surfer again. How can I export it from there as an Image file? The export function is currently greyed out.

Simply click the Map | New | Image Map menus and select the output GRD file you just created.

[Karsten Goemann]

Thanks, that worked great!
Is there a simple way to export the mosaic from Surfer in "original" resolution, i.e. maintaining the original pixel size without recalculation?

[Probeman]

Thanks, that worked great!
Is there a simple way to export the mosaic from Surfer in "original" resolution, i.e. maintaining the original pixel size without recalculation?

Did you try the File | Export menu? 

The default for the mosaic I exported was originally some 4000 pixels square but I reduced it to make a smaller file size, though you can just use the suggested resolution. Remember in Surfer, the graphs are all vector objects so the pixel size of the export is arbitrary.

[Karsten Goemann]

Yes, I tried File | Export but the suggested export resolution in there was much lower than the actual image resolution. It will be very difficult to calculate the actual resolution manually.

[Probeman]

Yes, I tried File | Export but the suggested export resolution in there was much lower than the actual image resolution. It will be very difficult to calculate the actual resolution manually.

Ok, I see.  So you would like to determine the acquisition pixel size in Surfer "page units"?   This does sound difficult.  I could ask Golden Software if there is a function to determine this (I think there must be).

But in the meantime I would just keep increasing the pixel export size until you see the actual acquisition pixels in the exported jpg file.

For example this zoom from my mosaic at 8192 x 8499 pixels:

[Karsten Goemann]

Thanks John, I basically just want a 1:1 acquired to exported pixel resolution, i.e. no mathematical operations performed on the pixels. Basically raw data but stitched to a mosaic. "Binning", e.g. combining 4 (2x2) acquired pixels into 1 would be OK, but only integer numbers for resolution reduction.

[Probeman]

Thanks John, I basically just want a 1:1 acquired to exported pixel resolution, i.e. no mathematical operations performed on the pixels. Basically raw data but stitched to a mosaic. "Binning", e.g. combining 4 (2x2) acquired pixels into 1 would be OK, but only integer numbers for resolution reduction.

The GRD file from the mosaic operation in Surfer contains exactly that information. No more, no less.

Try playing with the output grid in Surfer and see what you can find. There is also an ASCII output.

[Karsten Goemann]

OK, thanks, I will. If Surfer can't do it maybe I can import the output.GRD into ImageJ or something. A direct 1:1 .GRD to .TIFF conversion would be nice.

[John Donovan]

Hi Karsten.
OK, I fixed the "non-corner" image calibration issue. Actually I did more than that- now the mosaic feature will work with any type of calibration file: 2 points, 3 points, corner or non-corner...

Here's the file you sent loaded as an image (note the sub image horizontal field width field):



And here it is loaded as a sub image with the default mosaic loaded (not that anyone would actually mosaic their entire sample holder!):



Next I'll implement a z-tilt correction for the mosaic acquisition, though for SE and BSE imaging it isn't really necessary.

[John Donovan]

Of course the same is true of JEOL instruments (even though everything is "anti-Cartesian"!).   



In fact now the software moves the stage to your image and automatically rescales the magnification automatically starting with the lowest magnification:



Of course then you can manually adjust the mag if desired:

[Probeman]

In fact, if anyone would like these full size scanned sample holder jpgs shown in the above posts, the JEOL one is from Ma Chi at Cal Tech and the Cameca one is from Karsten Goemann at Hobart.

They are attached below (remember: you have to be logged in as a member to see attachments!).

Finally, in addition the program now automatically moves to the proper Z stage position if using a three point calibrated image and it is loaded "full size".   

[John Donovan]

Has anyone tried to mosaic the sub images together by using the Overlap parameter and an "image stitching" software package (as opposed to relying on the PFE image beam scan calibration)?  There are many free packages out there but I have not tried any of them:

http://en.wikipedia.org/wiki/Comparison_of_photo_stitching_software

Anyway, if you do want to try this, here is the overlap set to 5%:

[John Donovan]

Note that the Stage application was designed for confirming positions only, not acquisition. The Conditions, Sample Setups, File Setups buttons are for assignments only.

Now one might reasonably ask: why then is it there?  And the answer is: some people like to digitize off-line on an optical microscope and also do the condition/sample assignments off-line.

However, for image/mosaic acquisition in Stage, just set the instrument conditions in PFE or on the instrument console.  You can also use the Use Auto Brightness/Contrast checkbox to help compensate for variation in samples.

[Gseward]

I've also tried concatenate in ProbeImage. It seems I have to load the .GRD files so that it recognises the position registration. Is there a way to import them all at once? So far I've only found how to import them one by one, so I just imported the first two frames. When I then try to use the concatenate function, Probe Image crashes ("has encountered a problem and needs to close"). This is using Probe Image 1.1.0.1867.

Yes, Brian is aware there is a bug when trying to concatenate GRD files in Probe Image and is working on that. He is also adding GRD files to the "drag and drop" function and also adding a menu item to "Open All Files In Folder" menu.

this bug is still present. I  observe that images in x will mosaic, but as soon as I add the next row and try to mosaic (i.e. increment in Y) the program crashes.

[John Donovan]

Following suggestions from Anette and Gareth I added a new button in the Stage mosaic imaging window as seen here:



This will be very useful to specify the imaging parameters for the mosaic acquisition and also acquire a few single test images for getting the brightness and contrast *just right*.