HowTo wishlist

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- [ ] 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](https://github.com/imglib/imglib2-ui/blob/8ef079228b8a001789c150d99e5eaa708409472d/src/main/java/net/imglib2/ui/SimpleInterruptibleProjector.java#L194-L201) and discussed [here](https://forum.image.sc/t/enhance-local-contrast-parallelization-running-on-gpu-running-faster-anyhow/31996/5).
- [ ] How to [measure](https://gist.github.com/haesleinhuepf/a6c2a267bac15ea1c067f47e039acb66) resulting in a table ([related](https://github.com/mpicbg-scicomp/BioImageAnalysisToolbox/blob/master/src/main/java/de/mpicbg/scf/labelhandling/OpsLabelAnalyser.java))?
- [ ] How to deal with [image calibration / pixel size in space and time](https://git.mpi-cbg.de/rhaase/abia_prague_2019/blob/master/03_example_code_and_data/read_image_properties.ijm)?
- [ ] How to [visualize a spot detection result](https://gist.github.com/haesleinhuepf/79506120e5961eee8c2f56d3fc8618e5)?
- [ ] How to [save an animated GIF](https://github.com/haesleinhuepf/zoodirector/blob/master/src/main/java/net/haesleinhuepf/imagej/zoo/Thumbnailer.java#L210-L226)?
- [ ] How analyse an [MRI-data](https://git.mpi-cbg.de/rhaase/abia_prague_2019/blob/master/03_example_code_and_data/banana.zip) set of a [banana slice by slice](https://git.mpi-cbg.de/rhaase/abia_prague_2019/blob/master/03_example_code_and_data/analyse_banana.ijm) 😉
- [ ] How to [react on user clicks](https://github.com/clij/clij-advanced-filters/blob/master/src/main/java/net/haesleinhuepf/clijx/gui/ImageRegistration3D.java#L381) in an image window?
- [ ] How to [sychronize BigDataViewer windows/panels](https://github.com/clij/clij-bdv/blob/master/src/main/java/net/haesleinhuepf/clij/gui/bv/bdvtools/BDVUtilities.java#L98-L107) so that their planes are always perpendicular?
- [x] How to open [confocal series zip](https://imagej.nih.gov/ij/images/confocal-series.zip)
- [ ] How to iterate a [HyperSphere](https://github.com/imagej/imagej-scripting/blob/master/src/main/resources/script_templates/Tutorials/Create_and_Convolve_Points.py#L31) in Java - I only know the [cursor way](https://github.com/imagej/tutorials/blob/adding_scripting_templates/howtos/src/main/java/howto/processing/CreateAndConvolvePoints.java#L61).
- [ ] 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](https://imagej.net/docs/guide/146-30.html#toc-Subsection-30.2), including (or linking to) several steps:
- [ ] Threshold an image ([this notebook](https://github.com/imagej/tutorials/blob/2a09e6055f59c426ed95489d7eb36bff5be5f134/notebooks/1-Using-ImageJ/Ops/threshold/threshold.ipynb))
- [ ] Connected-component analysis ([this notebook](https://github.com/imagej/tutorials/blob/2a09e6055f59c426ed95489d7eb36bff5be5f134/notebooks/1-Using-ImageJ/Ops/labeling/cca.ipynb))
- [ ] How to take an `ImgLabeling` and iterate over its `LabelRegion`s
- [ ] How to get from a `LabelRegion` to a `RealMask` (i.e. `imglib2-roi`)
- [ ] How to do measurements on objects, using `RealMask`s 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-

Choose one unchecked HowTo rather than addressing the whole wishlist. Start with its linked example, notebook, or source file, such as the threshold and connected-component notebooks or CreateAndConvolvePoints.java. Add a focused tutorial that demonstrates the selected workflow and can be followed independently; the issue does not define a specific file, format, or completion target.

Written by the indexing model from the issue text.