Saving images with stage points from multiple samples

[Anette von der Handt]

Hi John,

I use extensively the annotated image function for setting stage points and documentation, specifically when running analyses for external users. I have two questions and/or requests:

a) Is there a way to show the points for multiple samples on a single image? I could swear that once upon a time it would just show all the points that occur in a given image but now it only shows the ones associated with a sample. I don't know what changed. I use different sample setups, so usually have multiple samples related to a given image frame. After image acquisition, I add new samples with the yellow button in the digitize image window because that seemed to associate the samples with the image. However right now, I have to manually associate the image with the individual samples one by one and export them via "Output". Ideally I would like to control what points are shown on a given image by selecting the samples (via shift-click?) in the "Display, annotate... window.

b) Also, the stage points are not saved with the image when using the "Save as BMP file" option (which allows me to save individual files and not the entire batch like under "output". Ideally I just would like to have the image saved "as is" meaning with whatever I choose to display. Instead only the bare-bone image is saved (without title, scale bar, points etc.).

Help Obi-John. What am I doing wrong?

[John Donovan]

a) Is there a way to show the points for multiple samples on a single image? I could swear that once upon a time it would just show all the points that occur in a given image but now it only shows the ones associated with a sample. I don't know what changed. I use different sample setups, so usually have multiple samples related to a given image frame. After image acquisition, I add new samples with the yellow button in the digitize image window because that seemed to associate the samples with the image. However right now, I have to manually associate the image with the individual samples one by one and export them via "Output". Ideally I would like to control what points are shown on a given image by selecting the samples (via shift-click?) in the "Display, annotate... window.

The answer is "yes". Simply click the All Positions option and all analysis positions within the image area will be displayed as seen here:

b) Also, the stage points are not saved with the image when using the "Save as BMP file" option (which allows me to save individual files and not the entire batch like under "output". Ideally I just would like to have the image saved "as is" meaning with whatever I choose to display. Instead only the bare-bone image is saved (without title, scale bar, points etc.).

Help Obi-John. What am I doing wrong?

Easy it is... utilize this menu one must:



The force be with you! 

[Anette von der Handt]

a) D'oh, totally missed the "all positions" option (forest - trees and so on). Thanks that solves it and makes my live much easier.

b) But, but, then I have to export all of them and not just the one I want. Anyway, as b) as a problem was directly related to a) and this one is solved, this works for me.

The force will be with me. Always. 

Thank you!

[jtmitchell]

Hi there, is it possible to retroactively export the images with the positions marked on them or does the option have to be selected right at the start?

[John Donovan]

Hi there, is it possible to retroactively export the images with the positions marked on them or does the option have to be selected right at the start?

If by "retroactively" you mean in "off-line" mode then yes, you can export images with analysis positions marked on them in "on-line" mode, or in "off-line" mode.  In other words, whether you are connected to the instrument or not as shown here:

https://probesoftware.com/smf/index.php?topic=278.msg1310#msg1310

The only caveat is that if you are re-processing data on an off-line computer or laptop, you will need to have both the MDB file of your probe run (which contains the point information) and the BIM image file (which contains the images) on the off-line computer.

Note that once you set your image export options from the Run | Display, Annotate, Export menu dialog, you can then go to the Output | Save Images To BMP and GRD Format  menu to export all the images automatically with the specified options.

[jtmitchell]

If by "retroactively" you mean in "off-line" mode then yes, you can export images with analysis positions marked on them in "on-line" mode, or in "off-line" mode.  In other words, whether you are connected to the instrument or not as shown here:

https://probesoftware.com/smf/index.php?topic=278.msg1310#msg1310

The only caveat is that if you are re-processing data on an off-line computer or laptop, you will need to have both the MDB file of your probe run (which contains the point information) and the BIM image file (which contains the images) on the off-line computer.

Note that once you set your image export options from the Run | Display, Annotate, Export menu dialog, you can then go to the Output | Save Images To BMP and GRD Format  menu to export all the images automatically with the specified options.

Thanks John, that's great!