Suggestion for tools to include in publication

[JochenGehrig]

Lets discuss the set of tools we want to publish in this thread. I suggest the following:

In an Fiji update site:

• VO_(input_image).py

• VO_Utils.py //not sure that will be needed if VOUtils.py(Batch) can handle folders with single images

• VO_(user_annotation).py

• VO_(inputimage)(Batch).py //only keep if there is a clear documentation. Currently, i dont know how to test it without looking at your code.

• VO_(userannotation)(Batch).py //very useful tool and probably the tool most people will use. I would ... :-)

• VOUtils.py(Batch) //not existant yet, but it should. see also https://github.com/sankeert1999/Virtual_orienation_tool_FIJI/issues/15#issuecomment-1814457547. Should provide the functionality to select 2 input dirs (raw images and masks) and 1 output dir.

the last 2 tools I would expect to be the most useful ones for end-users. Non-batch versions for developers.

Supplement(e.g. zenodo or osf or github etc)

• microscopy example dataset (raw data & pre-segmented); A nice and relevant dataset!!!
• zebrafish example script for segmentation
• zebrafish example data for segmentation; A nice dataset!!! No dead/rotting embryos, no embryos incompletely hatched, no embryos with edemas, heads coarsely to the left and dorsal to the top, transparent plate,

[LauLauThom]

VO_Utils.py is a file with utilitary functions used by the rest of the VOT plugins to avoid rewriting the same code. It has some test code too (hence the #@ notations at the top) but these are ignored when using the plugins.

So there wont be a VO_Utils (Batch) most likely, rather we will put more stuff in the current Utils to address the batch. Long story short this file has to shipped anyway 😅

EDIT : maybe clearer to say that the Utils file wont appear in the menu, but since Sankeert just shared the file like that it was not really clear that it is not supposed to be executed directly.

[JochenGehrig]

In whatever way it will be implemented i think a tool to select two folders would be nice. Similar to the current select a single image path function in the not-to-be-used VO_Utils.py; that is why i named it like that. Just to make it accessible for the guys who dont know how to loop over two different folders by writing code themselves ...or who dont want to or are too lazy etc ;-)