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README.md
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README.md

Focus_check script generates whole-plate montages per channel for inspecting data quality.

PUBLICATION: Yang, S. J., Berndl, M., Ando, D. M., Barch, M., Narayanaswamy, A. , Christiansen, E., Hoyer, S., Roat, C., Hung, J., Rueden, C. T., Shankar, A., Finkbeiner, S., & and Nelson, P. (2018), "Assessing microscope image focus quality with deep learning", BMC BioInformatics 19(1).

Link to publication: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2087-4

INSTALLING MACRO: https://github.com/fiji/microscope-image-quality

Fiji macros are scripts that increase throughput of image analysis, similar to that of already existing plugins. There are two ways of creating a macro: opening and editing an existing macro or recording your steps as you go through a protocol.

OPEN AND EDIT EXISTING MACRO:

  1. Go to PLUGINS > MACROS > EDIT...
  2. Find desired protocol and open
  3. Edit desired protocol and save

RECORD STEPS:

  1. Go to PLUGINS > MACROS > RECORD...
  2. Make sure at the top of the recorder pop-up window:
  3. "Record: Macro"
  4. "Name:" is set to the desired name of your macro (ex. "Focus_Quality_Check"). You do not need to include the extension as you can add that later when saving your macro
  5. Start going through your protocol, step-by-step
  6. Hit "Create" at the top of the recorder pop-up window
  7. Save your protocol

Once you are done creating your protocol, hit "Run" at the bottom of the editor window.

TO DO: (comment by samuely) Have one master script that we add flags for turning on/off certain features, such as the "single site" analysis or "with percentage". Since a lot of code is shared, it's easier to keep track of a single file. Documentation about the various flag options can go in the code rather than in this doc.