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Software Open Access

ModularImageAnalysis (MIA)

Cross, Stephen John

  • Added headless mode to allow workflows to be run without the need for opening a graphical instance of Fiji. This enables running MIA on terminal-only systems such as compute clusters. For more information see the guide at
  • The "MIA (headless)" menu option can also be used to run existing workflows with a minimal graphical interface and provides a method for launching workflows from ImageJ macros
  • Added modules to load and save objects to ImageJ .roi and .zip (zipped ROI) files
  • Included StarDistDetection module from mia-deeplearning repository. This module will only appear if StarDist update site is enabled
  • Projection axis cannow be specified in ProjectImage. This module also switched to primarily using ImgLib2. ProjectImage also outputs average projections as 32-bit
  • Updated handling of modules with incompatible dependencies. Now such modules aren't flagged at launch of MIA; instead, inactive modules are listed in both "Unavailable modules" section of "Add module" menu and via "Help > Unavailable modules" menu. Missing modules are still flagged when loading workflows that call for them
  • Minor website formatting updates and removal of "html" from URLs
  • Added many "MethodSource" tests for image processing modules. These are needed in the transition of these modules to ImgLib2
  • General bugfixes
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