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Several image processing workflow examples

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Several image processing workflow examples

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General workflow

The image processing work is usually revolving around the same concepts. This diagram (click for a larger view) show you what to do at which stage of your experiment, using ImageJ as reference software package.

Image J | Fiji based

Basic workflow

Once you are fixed on what you want to achieve, the processing steps usually involve the following:

  • Open the file → File>Open… or Bio-Formats
  • Check the file calibration → Image>Properties
  • Convert the file into a usable format (usually splitting channels and using 8-bit grayscale images) → Image>Color>Split Channels
  • Make copies → Image>Duplicate
  • Clean up the images → Image>Filter>Median
  • Segment the image → Image>Adjust>Threshold…
  • Setup the desired measurements → Analyze>Set Measurements
  • Create ROIs on the binary images → Analyze>Particle Analyzer
  • Apply these ROIS on the original images → ROI Manager>Show All with the original selected
  • Do measurements → ROI Manager>More>Multi-measure
  • Export Results → Results>Save as… using the CSV file format

You can then try to automate the process using macro recording or scripting. See  for more info on macro programming and automation.

More techniques

ImageJ’s “Learn” section is full of nice examples on specific techniques:

Advanced workflows (application based)

Recommended Book:

See also


Fiji’s Youtube page :

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