create stacks of micrographs for tomography

[fjchichon]

• tomography related projects use as input stacks of micrographs.
• it would be ideal to create a protocol that from a set of micrographs creates a set of stacks of micrographs

Input movies have the name xxxxx_YYY[angle]_Fractions.mrc

where xxxxx is fixed string, YYY is a 3 digit number that identifies the movie and angle is the acquisition tilt angle.

(@delarosatrevin, @rmarabini mention to me that you are working in the tomograpy data model and you may be interested in knowing this request)

I enclosed a script creates the stacks:

!/bin/bash

FOLDERS

ROOTFOLDER=/HOME2/2018_02_27_fcojavierchichon_t7_tomo INPUTFOLDER=$ROOTFOLDER/GRID_09/DATA IMODFOLDER=$ROOTFOLDER/IMOD

if [ -d $IMODFOLDER ]; then echo "$IMODFOLDER exist" else mkdir $IMODFOLDER fi

echo $ROOTFOLDER echo $INPUTFOLDER

BUCLE======================

cd $INPUTFOLDER for i in T7php??.txt;do

VALIABLES 1---------

name=${i%.*} TOMOFOLDER=$IMODFOLDER/${name}

____

CREATE FOLDERS

if [ -d $TOMOFOLDER ]; then echo "directory $TOMOFOLDER exist" else mkdir $TOMOFOLDER fi

_____

VARIABLES DEPENDING ON DE TOMOGRAM

TOMO number

TOTAL_tilts=ls $INPUTFOLDER/${name}*_Fractions_aligned_mic.mrc | wc -l NEGtilts=`ls $INPUTFOLDER/${name}???[-*_Fractions_aligned_mic.mrc | wc -l POS_tilts=echo "$[TOTAL_tilts - NEG_tilts -1]"`

TOMO files array

NEGfiles=`ls -r $INPUTFOLDER/${name}???[-_Fractions_aligned_mic.mrc ZERO_file=ls $INPUTFOLDER/${name}_001_Fractions_aligned_mic.mrc POS_files=ls $INPUTFOLDER/${name}_*_Fractions_aligned_mic.mrc | tail -n $POS_tilts`

CREATE SORTED list para newstack and RAWTLT file fron namefiles

FIRST line number of lines=number of tilts

echo "$TOTAL_tilts" > $INPUTFOLDER/${name}_sorted.txt

RAWTLT genetation blank

if [ -e $TOMOFOLDER/${name}.rawtlt ]; then rm $TOMOFOLDER/${name}.rawtlt else touch $TOMOFOLDER/${name}.rawtlt fi

echo "" > $TOMOFOLDER/${name}.rawtlt

NEGATIVES

for file in $NEG_files; do

tilt_image

echo "$file" >> $INPUTFOLDER/${name}_sorted.txt

slice into file

echo "0" >> $INPUTFOLDER/${name}_sorted.txt

tiltfile

tilt=echo $file | cut -d"[" -f 2 | cut -d"]" -f 1 echo "$tilt" >>$TOMOFOLDER/${name}.rawtlt done

ZERO

echo $ZERO_file >> $INPUTFOLDER/${name}_sorted.txt

slice into file

echo "0" >> $INPUTFOLDER/${name}_sorted.txt tilt=echo $ZERO_file | cut -d"[" -f 2 | cut -d"]" -f 1 echo "$tilt" >>$TOMOFOLDER/${name}.rawtlt

POSITIVES (using tile -n POS_tilts

for file in $POS_files; do

tilt_image

echo "$file" >> $INPUTFOLDER/${name}_sorted.txt

slice into file

echo "0" >> $INPUTFOLDER/${name}_sorted.txt tilt=echo $file | cut -d"[" -f 2 | cut -d"]" -f 1 echo "$tilt" >>$TOMOFOLDER/${name}.rawtlt done

GERERATE mrc STACKS with IMOD

if [ -e $TOMOFOLDER/corrected${name}.mrc ]; then rm $TOMOFOLDER/corrected${name}.mrc $TOMOFOLDER/${name}.st fi newstack -fileinlist $INPUTFOLDER/${name}sorted.txt $TOMOFOLDER/corrected${name}.mrc newstack -bin 2 $TOMOFOLDER/corrected_${name}.mrc $TOMOFOLDER/${name}.st

COPY Settings file to IMOD folders

cp $INPUTFOLDER/${name}.txt $TOMOFOLDER/${name}.txt

done

[delarosatrevin]

Dear @fjchichon, thanks for sharing this script!

When you talk about Stack of Micrographs...are you thinking in TiltSeries? My idea is to start testing the design of the data model for tomo. @cossorzano already had a good document that we can start with, but with some stuff from x-ray tomo that we might want to clean up first.

Can you explain (briefly, in text) what you scripts does (without the details) and the basic protocols for tomo/subtomo that you would like to see in Scipion?

[n1kt0]

Dear @delarosatrevin, Would you be so kind to share the script from @cossorzano you mentioned? I would like to look into that topic.

[delarosatrevin]

Hi @n1kt0 , The script is shared already in the first post of this issue. I was talking about Tomography Data Model...but we haven't started the implementation yet...but we are going to start working on it soon.

Are you interested in testing/working with some pre-processing protocols for Tomography we are start to implement in Scipion?

[n1kt0]

Since I'm an computer scientist working in tomography and have experience with IMOD and other tomography tools like tools for subtomogram averaging I would also be interested to integrate or help to integrate that stuff, I need only to learn more of the architecture of scipion to implement it conforming to the architecture. Some pointers where to look are appreciated.