docs: update scripts/README.md

cellacdc/scripts/README.md

@@ -1,32 +1,32 @@
-### Scripts to correct shifts in bidirectional scanning
+# Scripts to correct shifts in bidirectional scanning
 Using a bidirectional microscope can cause shifts in every second x-axis, resulting in extremely bad segmentation and tracking performance.
 These scripts correct this.
-### Work-flow
+# Work-flow
 Run this **before** dataprep but after creating a structure out of microscopy file.
 ## If you have multiple positions
 1. activate the 'acdc' environment
 2. Navigate to 'cd \Cell_ACDC\cellacdc\scripts' (if you have installed Cell_ACDC in a different directory navigate to that directory first)
 3. Use 'python correct_shift_X_multi.py [path to folder] [initial shift]' to run the script. Path to folder would be for example "C:\Users\SchmollerLab\Documents\My_Data\Timelapse_exp\2022-08-04" when one of the .tif files is in "C:\Users\SchmollerLab\Documents\My_Data\Timelapse_exp\2022-08-04\Position_8\Images"
 4. The program will run, pay attention to the console for user input requests!
-# Notes
+### Notes
 After the program is finished, you can run the data prep module. Check before running it that all frames are fine now, as sometimes the sign of the shift changes for a few frames. In this case, you can use the 'correct_shift_X_single.py' script.
 Sometimes you need to use a negative shift!
 Most of the times (but not always) the shift is the same for all positions.
 The expected structure of the folder is as the "Create data structure" module from cell_acdc creates.
 
 ## If you have a single position
 As above, except in step 3. You need to run 'python correct_shift_X.py [path to tif file] [initial shift]'
-# Notes
+### Notes
 As above
 
 ## If you need to change single frames
 As above, except in step 3. You need to run 'python correct_shift_X_single.py [path to tif file] [initial shift] [start frame] [end frame]'
-# Notes
+### Notes
 As above
 Usually, the sign of the shift changes in these frames. Since you usually should have run a shift on the tif file before, now you need to shift it with twice the amount back. If the original shift was 3, now you need to apply a shift of -6!
 The numbers for the frames match exactly with the numbers shown in the data prep module, so the first frame is the first and not the zeroth.
 
-### Possible problems with solutions
+# Possible problems with solutions
 I get errors from 'imshow':
 Change 'PREVIEW_Z_STACK' and 'PREVIEW_Z' (see Configs) in the script to values that make sense for you. Worst case try 0 for both.  
 tif files are not found:
@@ -36,7 +36,7 @@ Refer to tif files are not found.
 The shift is different depending on where on one picture I'm currently at:
 No fix, usually this effect is low enough to not cause problems with segmentation and tracking.
 
-### Configs
+# Configs
 There are quite a few things you can change in scripts. To change them, change them in configs.json in the "scripts" folder. For the regex expression please find "regex.txt"
 ## Same in all scripts
 'NEW_PATH_SUF':
@@ -55,4 +55,3 @@ Same as in 'INCLUDE_PATTERN_TIF_SEARCH', but this regex expression is used to ma
 'FOLDER_FILTER':
 Filter which is applied in order to make sure only folders which contain tif files (and not for example the original microscopy file) are considered.  
 The first function 'finding_base_tif_files_path()' is used to find the base tif files. If your basic directory structure is different, change this function accordingly. 'root_path' is simply the argument parsed from user input. 'base_tif_files_paths' is the path directly to your main tif file which should be used to determine the shift. 'tif_files_paths' is the path to the folder in which they are contained.
-