MSI-Edge hole targeting questions
Added by Anchi Cheng almost 14 years ago
This is transferred from an e-mail question by Bob Grassucci
Hi Guys,
I have a few questions about hole targeting in Leginon. I am going through it step by step and seem to be running into problems or it might be my lack of understanding the system itself. I will be using it again next week but before them I want to get a few of the settings clear. Here is whayt I am finding.
1. Leginon/Hole Targeting/Original
I get a hole and load it as the template.
2. Leginon/Hole Targeting/Edge
I choose 1.5 sigma and 3000 which gives me circles where the edge of the holse are with a inner diameter of 23 and outer diameter of 28 as measured with the ruler.
3. Leginon/Hole Targeting/Template
I add rings with diameters 23 and 28 choose cross correlation and get vice sharp peaks.
How can I measure the intensity of the peaks? Where is the tool for that?
I click test and get no peaks.
4. Leginon/Hole Targeting/Threshold
I would imagine a high threshold would decrease the number of peaks and A low threshold increase them when testing. Is that correct? Again what range am I looking for i.e. where can I find the values of the peaks? Do I enter the value form step 2 i.e. 3000 as the threshold? I tried making the values very low and see no peaks in the next step.
5. Leginon/Hole Targeting/Blobs
I set the border value to 40 and get no blobs. I suspect the problem is with the threshold but making it very high or very low gives me nothing. I hit test whenever I adjust the parameters and get nothing. I am missing something basic here. Any thoughts? Thanks.
I would like to understand the program before I try to teach others how to use it and I am missing something here. Other questions I have are:
How do I take multiple images from a single hole and where do I set it to collect on film.
Replies (1)
RE: MSI-Edge hole targeting questions - Added by Anchi Cheng almost 14 years ago
The question under step 3. Use the tool on the left hand side of the ruler that has 42 writing on it (Please reference "The hitchhiker's guide to the galaxy" for why 42). With it activated, hover the cursor around the pixel or displayed target where you need information on.
The question under step 4. No, you do not enter the value from step 2 because the value in step 2 applies to the edge image. The value here applies to the correlation image generated in step 3. As for a good value, it took me a while, too, since I have not used MSI-Edge for a while. It is in unit of number of standard deviation above the mean. Therefore, say the correlation image stats says mean=159, Std_dev=108 and a solid area around the peak is above 700, I would use (700-159)/108 = 5.0.
Multiple images from a single hole: If you are thinking of multiple positions in the same hole, you should select multiple acquisition target in Exposure Targeting Node either manually or using a template to convolve the resulting targets from step 5 and parameters in /Hole Targeting/Acquisition. If you are thinking of multiple exposure at the same position such as defocal pair or film exposure followed by an CCD image, you would include multiple presets in the
Exposure node preset sequence.
To set to collect on film, Edit the preset in Presets Manager. There is a check box for "Use film". If no one in your group has used that option, better do some tests before putting in your precious sample because it does need special stuff from FEI to work.