TODO

A loose TODO list for Fiji
==========================

- fix Temporal-Color Code for recent ImageJ hyperstack breakage
- provide a Fiji exception handler that
	- suggests updating if Fiji is out of date; and then
	- suggest bug reporting if it is up-to-date.
- ignore JAVA_HOME by default, add an innocuous option to jvm.cfg to force system java (either by using JAVA_HOME or by specific path)
- include Piotr's parallel deconvolution plugins, StackReg and BoneJ
- fix merge channels with 4 grayscale images
- fix z-project, split channels for virtual stacks
- fix substack maker for hyperstacks
- provide preview for auto threshold plugin
- provide a plugin that runs another plugin with a range of parameters
- add an installer (translate the original WinGit installer to Java, using the
  progress infrastructure of the Fiji Updater; maybe need to use reflection
  to access java.util.prefs.WindowsPreferences)
- win: verify that console window stays open when falling back to system Java
- move Amira I/O into bio-formats already
- headless: should we activate "batch"?
- Segmentation Editor fails
- add script recorder for the new scripting languages
- check which Reader Plugins do not extend ImagePlus
- extend GenericDialogPlus to provide Help, Advanced button
- GenericDialog.addToolText()
- add tests (test that all plugins are found, test which image types
  they support, add regression tests, if file importers return ImagePlus)
- in ImageJA: what about a file extension based construct similar to
  HandleExtraFileTypes for save?  This would allow to work on top of custom
  file formats seamlessly.
- look at ITK