Map grids (advanced)

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Name	Map grids (advanced)
Permalink	https://serialemscripts.nexperion.net/script/78
Category	High-Level Functions
Language	SerialEM Scripting
Description	This script allows the user to choose between mapping single or multiple grids from the auto loader as well as just mapping the grid that is currently on the compustage.
Author	Christian Dienemann

Version History

Version 1.0 (October 26, 2022; 251 download(s); SerialEM version ≥ 3.9)

Version 1.0

Download

Upload date	October 26, 2022
Download count	251
SerialEM version ≥	3.9

ScriptName Map Grids

SuppressReports

# The typical mag used for full grid mapping
mag_check = 135

#Values to simulate a full montage at the given mag
montage_x = 6
montage_y = 9
overlap = 180    # Overlaps needs to be 1px larger than in the full montage window... ?

# SD threshold to decide whether there is enough contrast for eucentricity
sd_treshold = 20

# Default starting directory if there is no navigator open
default_dir = X:

# Check the current mag
ReportMag
if $RepVal1 != $mag_check
   Pause The current magnification ($RepVal1) is different from the usual mapping magnification ($mag_check).
endif

echo ===> Define location for atlas and navigator saving

# Check if there is a navigator open already
ReportIfNavOpen

if $RepVal1 != 2
   # When there is no nav with a name
   OpenNavigator
   SetDirectory $default_dir
   OpenChooserInCurrentDir
   UserSetDirectory Choose the location to save atlas and navigator files
   atlas_folder = $RepVal1
   navfile = $atlas_folder\Navigator.nav
   
 else
   
   ReportNavFile 
   navfile = $RepVal1
   
   ReportNavFile 1
   atlas_folder = $RepVal3
   
   Pause The currently open navigator $navfile will be used and atlasses will be saved to $atlas_folder
   SetDirectory $atlas_folder
   
endif

echo Navigator will be saved to $navfile
echo Atlasses will be saved to $atlas_folder\Grid_[1-12].mrc

ParseQuotedStrings 1
header = 'How many grids to map?'

prompt1 = 'One (stage): map the grid that is currently on the microscope compustage.'
prompt2 = 'One (cassette): mat a single grid from the autoloader cassette.'
prompt3 = 'Many: map may grids by loading them from the autoloader cassette.'
buttons = {'One (on stage)' 'One (from cassette)' 'Many (from cassette)'}

ThreeChoiceBox header prompt1 prompt2 prompt3 buttons
method = $RepVal1 #1=one_cassette, 2=one_stage, 3=many

echo ===> Define which grids to be mapped

if $method == 3
   
   EnterDefaultedNumber 1 -1 START mapping at autoloader slot:
   start = $RepVal1
   EnterDefaultedNumber 12 -1 STOP mapping at autoloader slot:
   stop = $RepVal1
   EnterDefaultedNumber 15 -1 Waiting time (minutes) before starting:
   wait = $RepVal1
   EnterDefaultedNumber -1 -1 Grid to be loaded after mapping all grids (-1 = keep last):
   load = $RepVal1
   echo Mapping autoloader cassette slots $start to $stop
   if $load != -1
      echo Loading grid $load afterwards
   endif
   
 elseif $method == 2
   
   EnterDefaultedNumber 1 -1 Map grid from this autoloder slot:
   start = $RepVal1
   stop = $RepVal1
   echo Mapping grid $start from the autoloader cassette
   EnterDefaultedNumber 15 -1 Waiting time (minutes) before starting:
   wait = $RepVal1
   load = -1
 else
   # Put some standard values here
   start = -1
   stop = -1
   wait = 0
   load = -1
   echo Mapping grid that is currently on the compustage
   
endif

echo ===> Determine eucentricity?
YesNoBox Determine eucentricity before mapping?
eucentric = $RepVal1

OKBox Make sure you have retracted the objective aperture! Click OK to continue.

if $wait > 0
   echo ===> Initial wait to allow autoloader to cool down
   echo Waiting for $wait minutes...
   Delay $wait min
   echo Done.
endif

if $method != 1
   echo ===> Autoloader inventory
   echo Running inventory...
   LongOperation In
   echo Unloading grid from compustage...
   LongOperation Un
   echo Done. 
endif

DoLoop index $start $stop

## Get the grid for mapping

# Index is -1 if the grid currently on the stage should be mapped
if $index != -1
   
   ReportSlotStatus $index
   
   # When slot is occupied, load grid and collect atlas
   if $RepVal1 == 1
      
      LoadCartridge $index
      
   endif     
   
endif

MoveStageTo 0 0 0
SetColumnOrGunValve 1

# Only run this if wanted
if $eucentric == 1
   echo ===> Eucentricity
   # try finding enough light/contrast for eucentricity
   R
   ElectronStats A
   if $RepVal4 > $sd_treshold
      echo Found enough contrast, running rough eucentricity
      Eucentricity 1
    else
      echo Did not find enough contrast to determine eucentricity.
      echo Done.
   endif
endif

if $index == -1
   # Set the index to "stage" in case it was mapping a stage grid
   grid = stage
 else
   grid = $index
endif

# Sets the atlas file name
filename = $atlas_folder\Grid_$grid.mrc
# Move to the center to make sure the montage covers the whole area
# Simualte full montag ehere with command
OpenNewMontage $montage_x $montage_y $filename
SetMontageParams 1 $overlap $overlap
MoveStageTo 0 0
Montage 
NewMap
CloseFile
# Report last item
ReportOtherItem -1
ChangeItemLabel $RepVal1 Grid_$grid
LoadOtherMap $RepVal1 B
Try
SnapshotToFile -1 2 0 JPG NONE  $atlas_folder\Grid_$grid.jpg
Catch
echo There was a problem saving the snapshot image (likely not enough memory). See error in log above.
EndTry
SaveNavigator $navfile

endloop

# Make sure no open files remain
CloseFile

# Colose column valve
SetColumnOrGunValve 0

if $load > 0
   LoadCartridge $load
endif

Documentation

Features

- Mapping grids from autoloader (defined by start/end slot) or what is on the compustage
- Skips empty autoloader slots
- Option to determine eucentricity of the grid before mapping
- Opens a new navigator and saves it to a user defined location if there is no navigator open (uses currently open navigator otherwise)
- Grid maps are saved in separate files per grid
- A jpg snapshot is saved after mapping a grid (for visual inspection during the mapping)

Configuration

At the top of there script there are a few variables to configure:
mag_check : checks whether this mag is set before starting (e.g. a mapping imaging state)
montage_x : number of pieces in X to acquire
montage_y : number of pieces in Y to acquire
overlap : overlap between tiles in pixels (!)
sd_threshold : image value standard deviation threshold that defines whether there is enough contrast in an image to be used for the rough eucentricity task
default_dir : the default directory to be set when there is no navigator open

It might be necessary to experiment a bit with montage_x/y and the overlap setting to adjust to your imaging conditions.

License

This code can be shared and adapted under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) License (https://creativecommons.org/licenses/by-nc-sa/4.0/)