Trouble in MSI-Raster, sub-square targeting, Leginon3.1
Added by Ariane Fecteau about 9 years ago
Hi,
I want to image a 3-slot-grid with continuous carbon film (negative stain). I'm using MSI-Raster for this. At the subSquare targeting node, I establish poligon vertices and a raster (orange cross-hair) within these vertices. Then I would like to link an acquisition target to each orange cross-hair. I use the subsquare targeting settings window to do this and by pressing the test button. No green acquisition crosses appear. And the message "0 points with good ice" appear in the message window. (see image)
I'm using Leginon version 3.1, with Tecnai12 and TietzF416 camera
I've been trying a lot of different things and I'm at a point where I need some input!
Many many thanks!
Ariane.
Replies (1)
RE: Trouble in MSI-Raster, sub-square targeting, Leginon3.1 - Added by Anchi Cheng about 9 years ago
The problem in your settings is in standard deviation min/max.
The values here is based on a log(I0/I) scale, not the intensity value of the pixels. A few places in the wiki explains this Raster_finder_nodes_set-up, What_is_the_definition_of_ice_thickness_in_the_hole_finders, or Hole_Targeting_Set-up_for_MSI-T. The gui for RasterFinder is not as good as HoleTemplateFinders, but looking at how the latter works should help you.
There are two main reasons you get no acquisition targets pass the criteria. First, your "stdev min" is very large. Since in log scale 900 means I0/I is very very large, it corresponds to a very large differences in the pixel values in the box the statistics is calculated, which is unlikely the case for your data. Second, you "stdev max" is the same as "stdev min", which means you are not letting anything through as the program only wants what is in between the two numbers.
typical "stdev min" value is likely 0, and typical "stdev max" used to remove the targets close to a grid bar is likely 0.3-0.5.
You may also want to reduce "mean max" to more corresponds to log scale. That, along with a well-chosen "reference value", I0, is normally enough to remove targets land on the grid bar. You will not need to use the polygon tool at all.