Fiji runner for 1P Calcium imaging

Usage

./minizero_process.sh /path/to/Fiji.app/ImageJ-linux64 INPUT_FILE OUTDIR NAME

• INPUT_FILE: Video file (currently tested only with mio generated .avi files)
• OUTDIR, NAME: The exports will be {OUTDIR}/{NAME}_{PROCESSING_TYPE}

Steps

To do: Write more details

• Bandpass filter + autoscale
  • run("Bandpass Filter...", "filter_large=150 filter_small=1 suppress=Horizontal tolerance=1 autoscale process");
• 3D Gaussian blur
  • run("Gaussian Blur 3D...", "x=1 y=1 z=1");
• Bleach correction
  • run("Bleach Correction", "correction=[Histogram Matching]");
• Substack (for _*20)
  • run("Make Substack...", "slices=1-" + n + "-20");
• Background subtraction (for *_bg*)