Author Topic: PictureSnapApp version 1.7.3  (Read 2667 times)

John Donovan

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PictureSnapApp version 1.7.3
« on: February 10, 2018, 09:21:55 am »
We're pleased to announce a new software product, PictureSnapApp, for sample navigation for EPMA, SEM and TEM instruments.   Actually PictureSnapApp will work with any instrument that has an XY or XYZ stage, though we currently only have drivers for FEI, Cameca and JEOL instruments.

This is a very inexpensive application (US$499 for the hardware enabled version), and please note that in the *free* "Text Input" mode discussed below, PictureSnapApp will be useful on any instrument with an X/Y stage

Essentially this is a "standalone" version of the PictureSnap feature in Probe for EPMA, but designed to be utilized on various SEM, EPMA and TEM instruments (and any other instrument in the free "Text Input" mode), using an image of the sample or sample holder obtained from any optical (or other imaging) device. The idea is to be able to quickly take a picture of your sample holder, open it in PictureSnapApp, calibrate it, and navigate your sample holder in say, visible light.  For example, navigate quickly to the sample location with the brownish stain...

In addition PictureSnapApp allows one to annotate unlimited points and fields of view (FOV) *and* subsequently move your images and annotations to different instruments, easily recalibrate to the new instrument stage, and then accurately navigate back to those annotation coordinates or any other arbitrary sample location.

PictureSnapApp is available free for downloading here:

http://probesoftware.com/download/PictureSnapApp.msi

This free version of PictureSnapApp software has both a demonstration mode and also a text based input mode. The demonstration mode will allow everyone to play around with the software and see what it does, while the text input mode will allow PictureSnapApp to be utilized on any instrument, even if there is no hardware connection to the instrument stage.  Although the text input mode requires the user to enter the stage calibration coordinates using a keyboard.

For this $499 fee (per computer) we provide a registration number which will unlock the interface drivers for the FEI DCOM interface for all FEI SEM and TEM instruments, and also the EIKS interface for all JEOL SEM, TEM instruments (and also JEOL EPMA instruments for those that do not already have our Probe for EPMA product). We hope to add support for additional instrument vendor SEM/TEM stages soon.

Edit: We have now also added support for Cameca EPMA instruments if you don't already have our Probe for EPMA product or want the image annotation and image/stage transformation capabilities of PictrureSnapApp for moving images and annotations between different instruments...

Attached below (remember to login to see attachments) is a flyer describing the basic functions of the PictureSnapApp software. As a reminder, this app can import any JPG, GIF or BMP image up to 32K by 32K pixels for detailed sample navigation. For example the document camera described here is an inexpensive ($99) device for taking high resolution images of your sample or sample holder:

http://probesoftware.com/smf/index.php?topic=999.msg6635#msg6635

However, the image source can be from any device including other optical or beam instruments or even your cell phone camera!  In addition, any text annotations (which are calibrated in stage coordinates), will be automatically transformed if the files are transferred to another instrument and re-calibrated to that instrument's stage coordinate system.

But the best way to learn the software features and capabilities is to download it (it's free) and try it out! 

Please contact Barbara (barbara@probesoftware.com) for pricing and other details.

PictureSnapApp Version Changes:

09/15/2018    Add red annotation color.  Fix JEOL SEM stage orientation.
v. 1.7.3

09/13/2018    Fix bug in JEOL 8900/8200/8500 comms interface.
v. 1.7.2

08/24/2018    Modified the update download code to utilize https secure connections. 
v. 1.7.1

08/03/2018    Re-set the PictureSnapCalibration mode automatically back to two points when loading a new uncalibrated image.
v. 1.6.9

07/25/2018    Fix un-calibrated image bug in display current mag box code.
v. 1.6.8

07/19/2018    Modify GDI+ graphics to open/close in form load/unload events to prevent Microsoft memory leak.
v. 1.6.7

07/17/2018    Fix blinking problem with graphics drawing.
v. 1.6.6

07/11/2018    Modify ruler measurement feature to utilize GDI+ for anti-aliasing graphics.

07/08/2018   Add export of sub image ACQ calibration files from Image Locator window.
v. 1.6.5

07/07/2018   Add code to handle stage to image rotation for adding calibrated images and draw rectangle modes.
v. 1.6.3

06/29/2018   Add code to rotate annotations in PictureSnapApp transform menu dialog.
v. 1.6.1

06/27/2018     Add measurement tool to PictureSnapApp (Langworthy).
v. 1.6.0

06/20/2018     Add calibration accuracy output and Load ACQ from external file to Calibrate Image window.
v. 1.5.9

06/15/2018     Add "Select Remote Image" button to Image Locator feature.
v. 1.5.8

06/07/2018     Improve code to automatically handle updating of annotations and sub images after user clicks Calibrate Image. Add
v. 1.5.7            checks for stage tilt and FOV orthogonality.

06/03/2018     Add hand cursor for Image Locator feature to show pan/zoom capability. Fix image rotation display in Transform dialog.
v. 1.5.6

06/02/2018     Add image mosaic feature (in hardware enabled versions).  Add automatic conversion of point/FOV and sub image calibration coordinates from stage to screen. Makes the conversion to/from different stage systems better and *much* easier to code.
v. 1.5.5

05/26/2018     Resize image display for smaller images.
v. 1.5.4

05/23/2018     Add Image Locator feature with zoom and pan.
v. 1.5.3

05/16/2018     Improve stage config dialog, File Save As options.
v. 1.5.2

05/09/2018     Add additional tools for configuring and testing the FEI DCOM connection. Updated installation instructions.
v. 1.5.0

04/12/2018     Move stage to current position (if in bounds) when loading new image- just for moving main window to current position.
v. 1.4.9

04/07/2018     Add support for JEOL 8800/8900/8100/8200/8500 EPMA instruments (support for 8230/8530 instruments using
v. 1.4.8           existing EIKS interface.

04/01/2018     Add image rotation feature for when the sample must be mounted in a different orientation from another instrument.
v. 1.4.7

03/28/2018     Add digitize current position, rectangular/line drawing and new quick start popup.
v. 1.4.5

03/26/2018     Minor improvements.
v. 1.4.4

03/24/2018      Add support for "half-cartesian" stages (e.g., LA-ICPMS). Add support for "nm" units and also automatically convert images
v. 1.4.3            when loading them.

03/17/2018      Add "transform" dialog for unit conversion.  Stage orientation code next!
v. 1.4.2

03/15/2018      Add Cameca EPMA support. Minor improvements.
v. 1.4.1

03/09/2018      Add recently open file list and FOV annotations. Add Move To buttons for both point and FOV annotations.
v. 1.4.0

03/01/2018      Implement labels for calibration points. Improve annotation code (Seward).
v. 1.3.9

02/28/2018      Implement new options for defining the IP address of the instrument.  Add option to disable Z stage movement.
v. 1.3.8

02/12/2018      Fix missing file issue.
v. 1.3.6

02/10/2018      Add mouse cursor movement display of stage coordinates to full view image
v. 1.3.5

02/09/2018      Initial release of PictureSnapApp
v. 1.3.4
« Last Edit: September 15, 2018, 08:30:05 pm by John Donovan »
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macosta

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Re: PictureSnapApp version 1.3.5
« Reply #1 on: February 13, 2018, 02:27:09 pm »
 :)  :) :) :)

This app is bae.

I've been using the SEM/EPMA work for the past 8 years as both an undergraduate and a graduate student. My research has always required that I be able to correlate thin section images with SEM-CL/BSE/SE images, which can be challenging in the geologic samples that I work with.

In the past, I've had to do this by having a thin section high resolution scan of my sample pulled up on a separate computer, finding identifying markers to locate myself , collecting the images/data, and manually annotating the thin section scan with the approximate field of view in the SEM image and the SEM image file name.

As you can imagine, it can be quite time consuming. ADDITIONALLY, switching from the SEM, where I identified the phases I would like to analyze with either LA-ICP-MS or the microprobe I need to be able to verify that I am analyzing the exact crystals with the CL textures of interest, and the different zones of the CL in the individual crystal.

The PictureSnapApp streamlines this process, reduces the uncertainty, and is going to save me so much time! I  have used it twice now, and it is convenient and I'm able to collect data so much more efficiently.

The field of view is automatically outlined in the app, and resizes as you change magnification.

There is an annotation feature that I use to record all relevant information. The annotated image is easily exported as a BMP file.

The calibration is easy and painless. Instead of guessing my approximate location on the high-resolution thin section scans, I know automatically and with more precision EXACTLY where I am on my samples.

Every lab needs this.


-Marisa Acosta
 Department of Earth Sciences
 University of Oregon
 
Marisa D. Acosta

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Re: PictureSnapApp version 1.3.6
« Reply #2 on: February 13, 2018, 02:41:43 pm »
Hi Marisa,
Thanks for the nice review!   I had to google "bae" to find out what it meant!    :)

I should also mention that Marisa is the grad student here that said to me last December when she was running on the Quanta: "why don't we have PictureSnap running on the SEM?"   So she is the impetus for this app development.
john
« Last Edit: February 13, 2018, 03:09:39 pm by John Donovan »
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Re: PictureSnapApp version 1.3.8
« Reply #3 on: February 28, 2018, 07:08:54 pm »
The latest version of PictureSnapApp ( 1.3.8 ) now allows one to define the instrument IP address in case the default IP address is not being utilized.

Normally all FEI instruments use the 192.168.0.1 address for the SEM instrument.  But Gareth Seward's FEI SEM uses a hosted network switch which was set to that address, while the SEM instrument itself is set to 192.168.0.2.  So now when one selects the FEI DCOM interface, the 192.168.0.1 address is loaded by default, but one can specify a different IP address if necessary.

Same goes for the JEOL EIKS interface. Normally the IP address of the JEOL computer (EIKS server) is 192.168.0.4, but I just bet that someone, somewhere is using a different IP address.  So we also added code to handle that situation.



In addition we also added an option to disable the Z stage axis for movement as seen here:



Why? Because Z is essentially arbitrary in SEMs and maybe we only want to navigate in X/Y space.  It's an option anyway.
« Last Edit: February 28, 2018, 08:40:08 pm by John Donovan »
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Re: PictureSnapApp version 1.3.9
« Reply #4 on: March 01, 2018, 06:25:53 pm »
The latest version of PictureSnapApp has improved annotation capabilities and now labels the calibration points (also true for PictureSnap in the latest Probe for EPMA v. 12.2.0).

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neko

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Re: PictureSnapApp version 1.3.9
« Reply #5 on: March 07, 2018, 07:46:10 am »
I take it the stand-alone PictureSnap doesn't work with the Cameca SX system yet? The version included with PfE works though, right?

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Re: PictureSnapApp version 1.3.9
« Reply #6 on: March 07, 2018, 08:13:13 am »
I take it the stand-alone PictureSnap doesn't work with the Cameca SX system yet? The version included with PfE works though, right?

Yes, PictureSnap is completely integrated into Probe for EPMA.  That allows for some nice features, such as display of digitized or acquired positions on the image.

Right now we just do hardware interfacing to JEOL and FEI SEMs/TEMs (and JEOL EPMAs). We could add support for Cameca instruments in the standalone version of PictureSnap(App), we just didn't think there would be much demand so we haven't made it a priority.  We'll probably do it eventually though.  Or you'all could just get PFE for your instrument!   :D

But you could also download PictureSnapApp and simply use it in "text input" mode which will "run" on any instrument!  Once you install it, simply go to the File | Stage Config menu and select text input for the interface type (and configure the units to "um" and set the stage limits and FOV appropriately for the Sx100) and you should be good to go.  You'll have to enter the X/Y stage calibration point coordinates by hand, but once you do calibrate the image, you can navigate by double clicking any spot on the image and the stage coordinates of that position are displayed, with buttons for copying to the clipboard.

So until we get  PictureSnapApp interfaced to the Cameca, you could simply install PictureSnapApp on the PeakSight computer, so you can easily cut and paste between PeakSight and PictureSnapApp.   Hey, at least it's free!    :)
« Last Edit: March 07, 2018, 08:16:06 am by John Donovan »
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neko

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Re: PictureSnapApp version 1.3.9
« Reply #7 on: March 08, 2018, 08:40:22 am »
It works! A little clunky to use the copy/paste but it works and is quite accurate (and precise!). This will save a ton of time with folks who have small features that they need to locate on "fun" thin sections.

The only possible recommendation I would make is to make middle click (or L+R click) work to scroll the image around the viewport via dragging, if you have an image that outscales your monitor, and don't want to use the full, (possibly scaled down) view. Of course, our monitors are sorta small so that may not be a problem with newer monitors.

At least I can show this to people and be like "and if we upgrade to PfE, it'll work *even better*!"

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Re: PictureSnapApp version 1.3.9
« Reply #8 on: March 08, 2018, 08:49:24 am »
Hi Nick,
Cool.  Sorry about having to use text input mode for now, but that's why text input mode is free!  We'll get the Cameca instrument interface implemented quickly- we just didn't think there would be any demand for it, so we just released it for JEOL and FEI instruments to begin with. 

On the dragging the main window around one can use the scroll bars of course, but even better I think is to simply double click on the full view window and the main window image will be automatically shifted to the area of interest.

We've also been looking into Zeiss and Hitachi instrument interfacing, but so far Zeiss says they want $9K for their API, so we can forget about that!   Still looking into the Hitachi SEM API, so has anyone utilized the Hitachi SEM API for their own coding projects?  I'd be very interested to hear.
john
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Re: PictureSnapApp version 1.4.0
« Reply #9 on: March 09, 2018, 12:50:37 pm »
The latest version of PictureSnapApp now has a recently opened file list (thanks Gareth), and also FOV annotations (thanks Marisa), to document the current FOV on the image as seen here:



To annotate the current FOV, simply type "<shift> f" and enter any text in the pop up dialog.  In addition we've added Move To buttons for both point and FOV annotation lists so one can select any annotation from the list and move to that location automatically as seen here:

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Re: PictureSnapApp version 1.4.0
« Reply #10 on: March 10, 2018, 10:32:57 am »
Here's what one of our grad students, Marisa Acosta, has been using PictureSnapApp for with her scanned thin sections on our Quanta SEM:



The cool thing is that when she takes the image and the calibration files to another instrument, say the TOF-SIMS, she can simply recalibrate the image to the SIMS stage and the point and FOV annotations are automatically transformed, allowing her to easily navigate to their locations even if she can no longer see the thin section in visible light anymore.
« Last Edit: March 11, 2018, 12:10:02 pm by John Donovan »
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neko

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Re: PictureSnapApp version 1.4.0
« Reply #11 on: March 13, 2018, 03:06:54 pm »
I am happy to report that thus far, our lab users have responded enthusiastically to this app, and I've spread it to another lab in the department that has a laser ablation stage (I'll let you know if it ends up working out for them - they have an old P4 dell running XP with a single tiny monitor so ... it should work but might be inconvenient to use).

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Re: PictureSnapApp version 1.4.0
« Reply #12 on: March 13, 2018, 03:30:57 pm »
I am happy to report that thus far, our lab users have responded enthusiastically to this app, and I've spread it to another lab in the department that has a laser ablation stage (I'll let you know if it ends up working out for them - they have an old P4 dell running XP with a single tiny monitor so ... it should work but might be inconvenient to use).

Hi Nick,
Thanks, good to know.

Just FYI, in addition to getting the interface to the Cameca working, we will be making a bunch of other changes later this week to PictureSnapApp.  For example, to facilitate moving from one instrument coordinate system to another, and allowing the user to transform images that are oriented differently in different instruments.

Still very much a "a work in progress"!    :)    So do feel free to let us know of any ideas you/they have.   Be sure to update PictureSnapApp frequently using the Help menu...
john
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Re: PictureSnapApp version 1.4.2
« Reply #13 on: March 17, 2018, 06:16:56 pm »
We have now implemented in PictureSnapApp, support for Cameca EPMA instruments.

For Cameca EPMA instruments you'll want to select "um" for stage units, cartesian stage orientation, and enter the appropriate stage limits +/- 26000 in X, +/- 41000 in Y and +/- 1000 for Z, and roughly 1000 um for the FOV at 100x.

Any questions, just let us know.
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Re: PictureSnapApp version 1.4.2
« Reply #14 on: March 17, 2018, 06:24:52 pm »
We just released v. 1.4.2 of PictureSnapApp which has a number of small improvements including a new menu to transform images from one coordinate system to another.



For example transforming from um (Cameca) to FEI or JEOL (mm) stages (and visa versa).  Because JEOL SEMs utilize a cartesian stage orientation, this transform dialog works fine moving to/from JEOL SEMs to other cartesian stage instruments such as JEOL and FEI SEMs.

But while you can run PictureSnapApp just fine on your JEOL EPMA, we haven't yet implemented the coordinate transformation code to handle transferring the anti-cartesian orientation of the JEOL EPMA images to/from a cartesian JEOL or FEI SEM (or to/from a cartesian Cameca EPMA).  We will release the orientation transform feature shortly, but in the meantime for transferring calibrated images between all other instruments (FEI, JEOL SEM, Cameca EPMA), the stage unit conversion works fine. Also the transform code automatically converts all point and FOV annotations.  See this Cameca image in mm units after conversion from um stage units:



When you click on the Transform menu you'll get this dialog:



As you can see, the conversion from um to mm was selected.  The image and calibration filenames are automatically appended with the unit conversion that was performed. e.g., "_um_to_mm" or "_mm_to_um" as seen here:



Please update from your Help menu and try it and and let us know what you think.
« Last Edit: March 17, 2018, 10:48:27 pm by John Donovan »
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