SerialEM Note: Adding Point Items by Template Matching¶
- Author
Albert Xu
- Contact
- Date_Created
2019-07-25
- Last_Updated
2019-07-25
- Abstract
This article describes a method of automatically picking points in SerialEM maps. Currently SerialEM does not have built-in functionality of adding points by correlation. However, SerialEM is now capable of running external Windows programs via the RunInShell script command, as well as merging in externally defined navigator items. This means that is it possible to use any external program to search for desirable points and add them to the navigator. As an example, I present a graphical tool called semmatch that uses cross-correlation based template matching. Hopefully in the future others will be inspired to implement their own methods and programs to improve the SerialEM user experience.
Install¶
A SerialEM script called TemplateMatch_GUI at the end of this article is
used to launch semmatch. All that is required is to install semmatch in
order to use the script. Installation instructions are on the github page,
https://github.com/alberttxu/semmatch
Usage¶
1. First, select a map item from the navigator. You can double click to load the image, or single click to simply highlight.
Before running the script, you can optionally crop out a template in
SerialEM. See TemplateMatch_GUI for details.
Run TemplateMatch_GUI
+/- to zoom in and out.
To crop, just click and drag.
Change the threshold and click search until you are satisfied with the result.
Click Save and Quit to merge the generated points into SerialEM. To quit without saving, close the window from the top.
ScriptName TemplateMatch_GUI
### Before running this script:
# (Optional) Save a template of a hole/pattern as a jpg image.
# 1. Crop a hole using ctrl+shift+drag,
# 2. Menubar->Process-> Crop Image.
# 3. Using the Edit/Run one Line prompt, run
# SaveToOtherFile A JPG JPG T.jpg
#
# If something goes wrong, set Debug = 1
Debug = 0 # True = 1 ; False = 0
### semmatch arguments
threshold = 0.8
acquire = 1 # True = 1 ; False = 0
groupOption = 4
# 0 = no groups
# 1 = groups based on radius
# 2 = all points as one group
# 3 = specify a certain number of groups
# 4 = specify number of points per group
# names of temporary files used by semmatch
outputNav = semmatch_nav.nav
image = MMM.jpg
template = T.jpg
ReportIfNavOpen
If $reportedValue1 != 2
Exit
Endif
ReportNavFile 1
navfile = $reportedValue1$reportedValue2
navdir = $reportedValue3
SetDirectory $navdir
If $acquire != 1 AND $acquire != 0
Echo acquire should be either 1 or 0
Exit
Endif
If $Debug == 1
debugStr = /k
ElseIf $Debug == 0
debugStr = /c
Else
Echo Debug should be either 1 or 0
Exit
Endif
## load and bin MMM map
ReportNavItem
If $RepVal5 != 2 # if not a map item
Echo Not a map item. Select a Map item from the navigator.
Exit
Endif
MAP = $navLabel
Echo Map Label: $MAP
SetUserSetting BufferToReadInto 16
SetUserSetting LoadMapsUnbinned 1
# uncheck Montage Controls "Align pieces in overview"
ReportUserSetting MontageAlignPieces alignChecked
If $alignChecked == 1
SetUserSetting MontageAlignPieces 0
Endif
LoadNavMap
# reduce image if larger than 2000x2000
maxdimLimit = 2000
ImageProperties Q width height
maxdim = $width
If $width < $height
maxdim = $height
Endif
If $maxdim < $maxdimLimit
Copy Q A
reduction = 1
Else
reduction = $maxdim / $maxdimLimit
ReduceImage Q $reduction
Endif
Show Q
## make a jpeg image
SaveToOtherFile A JPG JPG $image
Echo saved $image
ReportOtherItem -1
newLabel = $navIntLabel + 1
RunInShell cmd $debugStr " "semmatch" \
"--gui" \
"--navfile" "$navfile" \
"--reduction" "$reduction" \
"--image" "$image" \
"--template" "$template" \
"--mapLabel" "$MAP" \
"--newLabel" "$newLabel" \
"--threshold" "$threshold" \
"--groupOption" "$groupOption" \
"--output" "$outputNav" \
"--noBlurTemplate" \
"--noBlurImage" \
"--acquire" "$acquire" "
MergeNavFile $outputNav
If $alignChecked == 1
SetUserSetting MontageAlignPieces 1
Endif
Show Q