Jan Eglinger

Consider using Jupytext for version control of Jupyter notebooks

1

[Jupytext](https://github.com/mwouts/jupytext) looks like a good solution for version control of `.ipynb` notebooks, allowing clean version history in `md` or `py` and synchronising them with the rendered `ipynb` notebooks.

Include Maven installation of ImageJ and Fiji artifacts in postBuild for binder

6

Maybe we can run `mvn` (or `jgo`) in a `binder/postBuild` file to pre-install the Fiji and ImageJ Maven artifacts (at the versions used in the notebooks) at the time of...

Create tutorial about imglib2-roi and how to work with labelings

2

Documentation on the most recent features of `imglib2-roi` is still sparse. Some of it is in the [`roi-demo`](https://github.com/imglib/imglib2-roi/tree/roi-demo) branch, some other info is scattered across github issues or on gitter...

Add example command using parameter validation

1

In the [`dynamic-commands`](https://github.com/imagej/tutorials/tree/master/maven-projects/dynamic-commands/src/main/java) project, it would be useful to add an example illustrating parameter validation. Does some example like this exist already, and I missed it?

Separate environments for notebooks with and without python and imglyb

2

I suggest to somehow separate those notebooks requiring `python` and `imglyb` from the "pure" ImageJ tutorial notebooks and create two distinct `environment.yml` files. This would allow the startup of the...

Add CITATION file with bibtex entries

1

To help citing the ImageJ project, let's include a `CITATION` file in this repository (and possibly in other repositories where applicable). See some related discussion in https://github.com/CellProfiler/CellProfiler/issues/3480, as well as...

Default location of .jgo on Windows

2

On Windows, it seems that Maven puts its `.m2` folder into `%USERPROFILE%\.m2` by default, whereas the default location for `.jgo` is `%HOME%\.jgo`. This can be problematic in cases where `%HOME%`...

This is a reminder to *pleeease* migrate [`SwingGroupingInputHarvester`](https://github.com/scenerygraphics/sciview/blob/121e036477da69bb2706140297171105e94c1700/src/main/java/sc/iview/ui/SwingGroupingInputHarvester.kt) to `scijava-ui-swing` 😃 See https://github.com/scijava/scijava-common/issues/310#issuecomment-733918095.

Add option to change recording destination

1

Allow saving somewhere else than the desktop

Consider moving to ImageJ-MATLAB instead of Miji

2

As mentioned on https://imagej.net/plugins/miji, this legacy project is mostly replaced by the functionality in ImageJ-MATLAB: https://imagej.net/scripting/matlab#running-imagej2-within-matlab I don't know the usage of Miji in ciatah in detail, and I don't...