Macro_CV7000_Make_Time_Lapse_Movies - stoeter/Fiji-Tools-for-HCS GitHub Wiki

Table of Contents Macro CV7000 Make Time Lapse Movies Configuration Hints What the macro will do Log Window Issues Code Latest changes

• This macro is part of the "Automated Microscope Tools" macro set.
• This macro reads CV7000 images (.tif) of a time lapse measurement and creates movies as multi-page tif and/or AVI.
• This macro can be used to put all images of a time lapse measurement into one or few files.

1. Start the macro in Fiji under Plugins->Tools for HCS->Automated Microscope Tools->Macro CV7000 Make Time Lapse Movies
2. Select the folder of (CV7000) images (.tif; measurement folder!)
3. Select or create the folder for result images / movies
4. Dialog “Image File Filter...”
   1. Leave as default will select the first time point (T0001) for each position and well for extracting meta data. The groups of images will be loaded later differently!
   2. Define text that should be searched in the file path (e.g. "_B02_")
   3. Specify what should be dont if this text is found in path
   4. Including "_T0001" will also ignore correction images of CV7000 automatically.
      1. no filtering: nothing will be done
      2. exclude: file containing this text will be excluded from all files found
      3. include: only file are processed that contain this text
   5. Up to 3 consecutive filters can be applied and the output of one filter is the input of the next filter. (Note that filters are applied consecutively and list are not additive (e.g. 1) include GFP, 2) include DAPI will not result in a file list containing file paths with GFP and DAPI)
   6. If check file list is ticked windows with a file list after each filter will be displayd for trouble shooting.
5. Inspect the Log window...
   1. All options settings in this macro are recorded to the log and save in result folder
   2. Check the number of file are found for during filtering
   3. Remember that only the first point of a movie series is listed (T0001)
   4. Check the number of well fields (all imaging positions)
   5. Check if the listed meta data is as expected (well field, acquisition number, time lines, time line acquisitions)
   6. If there are problems check the "Display file lists" check box in previous dialog and go through the lists and click "OK" when you are done
6. Dialog "Settings for movie generation"
   1. Choose the file type to be saved for image series (.tif and/or .avi)
      1. For .avi compression can be set to: no compression, JPEG or PNG
      2. For .avi the number of frame per second can be set for a movie
   2. Select the acquisition numbers that should be loaded for the image series
      1. left example shows concatenation of acquisitions
      2. right example shows usage of color channels
   3. Define how to treat multiple acqusition numbers:
      1. "Keep separate files" will save images series of different acquisition numbers in separate files
      2. "Concatenate as series" will add image series of different acquisition numbers and save them in one file
      3. "Merge as channels" will save image series of different acquisitions as hyperstack file with color channels
   4. Define how to treat multiple time lines:
      1. "Ignore time lines": will not use time line meta data and all images are treated as one time line
      2. "Process time lines separately": will save image series of different time lines in separate files
   5. "Use channels instead fo acquisitions" will ignore the acquisitions metadate and will use instead the channel metadata. Having this ticked will also open another dialog for selection channels...
      1. Select the channel numbers that should be loaded for the image series
   6. "Adjust contrast and make 8-bit?" gives the opportunity to convert the images to 8-bit before saving. Having this ticked will open another "Set contrast..." dialog
      1. Define the color for each channel (red = 1, green = 2, blue = 3)
      2. Set the mimimum and maximum intensity value for contrasting (Hint: analyse the intensity rang by opening a single images of each channel before running the macro)
   7. Tick check box to not display loading and procession of images

• Try with the default settings, and a single well (image filter for e.g. _B02_) to see if the macro does what you want
• Check "Display file lists", go through the lists and also check the displayed meta data
• Make sure that you understood the CV7000 file naming and meta data completely -> CV7000 file names
• Check the Log Window when the macro is finish and see if the meta data / regex resembles your groups of image series

• First the image filter will find the first time point (T0001) of each group of image series
• From these first time point all meta data available is extracted (e.g. well field, time line, etc.)
• For all groups of well fields, time lines and acquisitions a regular expression is assembled
  • or for all groups of well fields, time lines and channels a regular expression is assembled
• Using the regex a series of images will be loaded
• If no images are found for a certain regular expression, the macro will ignore this and goes on
• Several image series can be concatenated or merges as color hyperstack
• Finally the image series are saves as .tif and/or as .avi intensity is saved to the log.

1. The log window will document all important information of the macro:
   1. Input and output directories
   2. Number of files that were found and number of well fields
   3. Number of unique meta data found in file names (acquisition, time line, time line acquisition)
   4. Save options and treatment or acquisitions and time lines
   5. Group of meta data defining the regular expression
   6. The regular expression used for loading image can be used manually in Fiji (File->Import->Image Sequence)
   7. Name of saved files
2. The log window will be saved as a log file (.txt) with time stamp in the result folder

- selection of 4 acquisitions or channels will for "merge channels" will give an error

The code you can find here.

• fourth release 31-03-2018: bug fix: only one channel was processed
• third release 14-11-2017: enabled the use of channels and contrasting for 8-bit convertion
• second release 27-03-2017: moved from development status to official relased