Isn’t a multi tab spreadsheet essentially 3d? The sheets can reference each other, and every sheet is an NxN slice of an NxNxN cubic space.
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Yes, though something that can render in 3D would be nice for visualizing what the data mean. And while that works for 3D, suppose you need something with a fourth axis. You would have to add another level of tabs to keep your tabs in for each new dimension. Not that you'd usually need more than like 5D, but still.
Python + pandas?
My first thought was matlab, but it might not have the string editing capabilities OP wants
That or numpy.
You can use multiple sheets in a workbook or multiple layers in an image editor to get a third dimension in existing 2D data editors. I've done some weird things like pack numeric data into RGB pixel values when I needed to annotate an image with a couple bytes of data per pixel in irregularly shaped regions...
If Minecraft is an actually serious possible solution to what you're doing, maybe a world editor for it would be useful? I don't know what's popular now (been OOTL for too many years) but people used to make custom maps in MCEdit; some of the 3D brush tools and such might be useful depending on what you're doing?
Can you provide more details on what you're trying to do?
Minecraft is not a serious solution. I could get it to work but it would be terribly uncomfortable to read and edit, almost certainly worse than layered 2D spreadsheets.
Currently i'm making a constructed language and trying to work out what all the possible syllables are given the fairly simple syllable structure. There are tools specifically for this, but there have been other times when a 3D spreadsheet would have been very helpful even if i can't still remember what problem i had.
Another example, also for constructed languages, is tables of conjugations and declensions in fusional languages. That is, a language where a single prefix or suffix indicates a specific case, person, number, etc. and there are a bunch of these that need to be mapped out.
Hmm. I see. I'm not aware of something that I think would be particularly good for that which already exists, but it's the kind of thing that sounds like it might be possible to hack together quickly with an HTML table, contenteditable (or input tags), a few buttons/select tags/etc, a bit of JavaScript, and maybe python3 -m http.server or a Python script using tornado depending on what was needed exactly... but maybe I've been in web programming land too long.
You might want to look into GNU Octave, it's like an open source version of Matlab which is often used for managing high dimensional data.
https://wikipedia.org/wiki/GNU_Octave
A couple other approach depending on the data and use are using relational database, storing the data in a database normalized form, then using a declarative style language like SQL to combine or exclude data in operations. And if it's mostly physics spacetime coordinates xyz+t tensor frameworks and libraries are built on top of most popular general purpose programming languages (python, c, java, etc) for that purpose.
SQLite or MariaDB? I know this is a lot more advanced to use than a regular spreadsheet but they are open source, work on Linux, and powerful for data organization.