LabAdviser/314/Microscopy 314-307/TEM/ETEM/OneView: Difference between revisions

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 '''Feedback to this page''': '''[mailto:labadviser@nanolab.dtu.dk?Subject=Feed%20back%20from%20page%20http://labadviser.nanolab.dtu.dk/index.php/LabAdviser/314/ETEM/OneView click here]'''
-(''content by Jens Kling, September 2021'')
+(''content by Jens Kling @DTU Nanolab, September 2021'')
 [[Category:314]]
 [[Category:314-Microscopy]]
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 - In our setup, the OneView camera exclusively uses the pre-specimen shutter in idle state (beam on the camera but camera not running), which means the sample is not illuminated.<br />
 <br />
+== Possible Issue ==
+We came across a strange behavior in GMS3 when acquiring images with drift correction on the OneView camera.
+We are specifically talking about the acquisition in general imaging mode. When the drift correction is used, GMS allows to "trim" the acquired image after drift correction to the area where all frames have information. This leads to smaller images than the general 4096x4096px and also uneven number of pixels in x- and y-direction. So far so good.
+Now it appears that when the trimming option is used, even though the images might have different number of pixels in x- and y-direction (and we are typically talking about maybe up to 20-30px), the software adjusts the lengths of the image to be square (f.ex. 73nmx73nm). This causes the pixel calibration in both directions, x and y, to be slightly different, which means, when you measure length in different directions, they differ.
+[[image:Trim-issue_20220704_Info.PNG|300x300px|left|thumb|Image information after trimming.]]<br clear="all" />
+[[image:Trim-issue_20220704_Info2.PNG|300x300px|left|thumb|Image information after trimming.]]<br clear="all" />
+[[image:Trim-issue_20220704_Info3.PNG|300x300px|left|thumb|Image information after trimming.]]<br clear="all" />
+You can avoid this by NOT using the trim function with the drift correction. Use the gear icon in the acquisition control panel in GMS and un-select the trim function.
+[[image:Trim-issue_20220704_trim.PNG|400x400px|left|thumb|Change drift correction settings.]]<br clear="all" />
+If you already have images that show this special "feature", you can try to re-calibrate your image afterwards. In the tags of the image you can find the actual magnification (not the indicated magnification). The pixel size on the camera is 15µm. Dividing the pixel size by the magnification gives you the length per pixel.
+We will bring this issue forward to Gatan but I don't expect any fast response/reaction. My strong suggestion would be, acquire without trimming!
 == Operation ==
 [[image:Gatan_OneView_1.png|400x400px|right|thumb|GMS3 main window.]]
-. If the computer for the OneView camera is not running (large screen), start the computer. It is located in the technical room behind the microscope (large computer with a lot of hard drive slots). The login is:<br />
+. If the computer for the OneView camera is not running (large screen), start the computer. It is located in the technical room behind the microscope (large computer with a lot of hard drive slots). The login can be found on the whiteboard.
-: user: '''Administrator'''<br />
-: PW: '''$admin'''
 <br />
 . If GMS3 (Gatan Microscopy Suite; also known as Digital Micrograph) is not running yet, click on the GMS icon and acknowledge any information message (elevated privileges; using potentially harmful plug-ins).<br />
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 * Each frame will be saved hierarchically in the folder under '''Hour_xx''', '''Minute_xx''', '''Second_xx'''.<br />
 <br />
 == Additional information ==