Macro_CV7000_Z Projection - stoeter/Fiji-Tools-for-HCS GitHub Wiki

Table of Contents Macro CV7000 Z-Projection Configuration Log and List Windows Issues Code Latest changes

• This macro is part of the "Automated Microscope Tools" macro set.
• This macro loads CV7000 images (.tif), allows the used to filter the file list and saves Z-Projections (6 methods) for the same wells fields and channels.
• The macro allows to choose which planes to use for a z-projection (choose first to last plane)

1. Start the macro in Fiji under Plugins-> Tools for HCS->Automated Microscope Tools->Macro CV7000 Z-Projection
2. Select the folder of CV70000 images (.tif; measurement folder!)
3. Select or create the folder for result image (z-projections)
4. Dialog “Image File Filter...”
   1. Leave as default will select only .tif images and will process all files found.
   2. Correction images of CV7000 (.tif) containing text "DC_sCMOS #" or "SC_BP" are automatically removed.
   3. Optionally specify the image file extension.
   4. Define text that should be searched in the file path.
   5. Specify what should be dont if this text is found in path
      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
   6. 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)
   7. If check file list is ticked windows with a file list after each filter will be displayd for trouble shooting.
5. Dialog “Set projection type”
   1. Choose between six different z-projection types: Max Intensity, Sum Slices, Average Intensity, Min Intensity, Standard Deviation or Median
   2. Select first (lowest) and last (highest) plane from entire stack to use for z-projection
   3. Set batch mode to not display the processing of images
6. Image sets are prcessed in the following order:
   1. per well
   2. per field
   3. per channel

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 fittet the filtering criteria
   3. Defined filter text and method and number of file after each filterig
   4. Number of wells, fields (and well field) and channels
   5. Number of planes that are used and type of z-projection chosen
   6. Each image path opened for a projection and path of the save z-projection
2. In addition list windows are optionally opened to check the filtering process (see above)
3. Windows listing the well, fields, well fields and channel are also displayed
4. The log window will be saves as a log file (.txt) with time stamp in the result folder

• Problems in no CV7000 file names are used like ..._G13_T0001F001L01A03Z01C01.tif (seach for "_T00")
• Slow processing of file list due to ImageJ macro language of funtions -> re-write in Java

The code you can find here.

• sixth release 29-04-2016: fix bug in for non-CV7000 images, filtering correction images