Faster progress on Micro-Manager development thanks to new AI coding tools

Like so many other software projects, Micro-Manager has benefitted enormously from the new AI coding tools. Development is often faster than documenting, and to rectify that a bit I am planning to write a couple of posts about new features in Micro-Manager. For me, but also for you the reader, first a short overview of accomplishments in the last 6 months or so.

Device Adapters added:

  • Evident IX85
  • Rapp UGA42 (plus Rapp lasers)
  • Spinnaker C (should be less dependent on Spinnaker version than the original Spinnaker adapter, by Mark Tsuchia)
  • Utilities - StageState device (so that a linear stage can be used as a state device, by Mark Tsuchida)
  • Thorlabs TSP01 temperature and humidity sensor (by @aandreev0)
  • iSIMWaveForms (by Kyle Douglass)
  • ReflectorFocus: Focus maintennace device that needs a camera, shutter and stage in the configuration.

User Interface added or expanded:

  • High Content Screening plugin: adds WellZoom window that shows zoomed in well including location of the stage within the well.
  • MultiChannelShading: makes it possible to remember shading settings for different magnifications (i.e for different objectives).
  • Added 3DScript to the 3D (ClearVolume) viewer. Also added a reel editor that generates a script from keyframes. Enables export to a movie using ffmpeg.
  • Adds support for 32bit (float) images in the viewer.
  • Much better support of RGB images in the viewer, including various facilities to set white and black point.
  • Adds Stitch plugin: automatically stitch acquisitions of multiple, overlapping positions. Includes automated image flipping/rotation based on affine transform, alignment and blending.
  • Adds Explorer plugin, similar to SlideExplorer and MicroMagellan, but fully integrated with the Micro-Manager UI. Allows for export of stitched and blended images.
  • Adds NavigationByMap: load a map of the sample, acquired anywhere at any resolution, set 3 points that correspond to locations on the current microscope and navigate to any position in the map.
  • iSIM plugin (by Kyle Douglass).
  • Deskew Explorer: Explorer for Snouty-type Light sheet microscopes, takes a volume at each position, projects and places in an Explorer.

I’ll go into detail for a few of these new features in the near future.