• How to loop over all images of a directory
• How to convert image types
• How to do maximum projection
• How to add overlays / work with ROIs
• How to parallelize image processing using the Executor service as done here and discussed here.
• How to measure resulting in a table (related)?
• How to deal with image calibration / pixel size in space and time?
• How to visualize a spot detection result?
• How to save an animated GIF?
• How analyse an MRI-data set of a banana slice by slice 😉
• How to react on user clicks in an image window?
• How to sychronize BigDataViewer windows/panels so that their planes are always perpendicular?
• How to open confocal series zip
• How to iterate a HyperSphere in Java - I only know the cursor way.
• How to carry out pixel level mathematical operations like I can in Matlab? Full access to indices, values, logical operations etc. (may be ask @lhilbert what exactly he means by that)
• How to use the Logger?
• How to take a RandomAccessibleInterval and open it in a new or a given pre-existing BigDataViewer.
• (as a HowTo or notebook) How to do particle analysis, including (or linking to) several steps:
  • Threshold an image (this notebook)
  • Connected-component analysis (this notebook)
  • How to take an ImgLabeling and iterate over its LabelRegions
  • How to get from a LabelRegion to a RealMask (i.e. imglib2-roi)
  • How to do measurements on objects, using RealMasks sampled on an input RandomAccessibleInterval; e.g. center of mass etc.

Who has more questions?

Can others edit this post? If not, just answer and I update the list. We could also add the user handle next to a question if someone volunteers to solve a specific one-