Update README with content from vistools

README.md

@@ -1,6 +1,63 @@
-# bigdataviewer-core
+![logo](../bigdataviewer-core/bdv-logo-dark-bg.png#gh-dark-mode-only)![logo](../bigdataviewer-core/bdv-logo-light-bg.png#gh-light-mode-only)
 
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-ImgLib2-based viewer for registered SPIM stacks and more
+# bigdataviewer-core
+
+ImgLib2-based re-slicing viewer for terabyte-sized multi-view image sequences.
+See https://imagej.net/plugins/bdv for (somewhat out-dated) user documentation.
+
+BigDataViewer is designed to be re-used as a visualization component in other software (besides being a stand-alone Fiji plugin).
+Examples include [ABBA](https://abba-documentation.readthedocs.io), [BigStitcher](https://imagej.net/plugins/bigstitcher), [BigWarp](https://imagej.net/plugins/bigwarp), [Labkit](https://imagej.net/plugins/labkit), [MaMuT](https://imagej.net/plugins/mamut), [Mastodon](https://imagej.net/plugins/mastodon), [MoBIE](https://mobie.github.io), [Paintera](https://github.com/saalfeldlab/paintera).
+
+# vistools
+
+The best entry point for using BDV in your own project is the [BdvFunctions](https://github.com/bigdataviewer/bigdataviewer-core/blob/master/src/main/java/bdv/util/BdvFunctions.java) class.
+A short introduction is below, and you can find a lot of short examples [here](https://github.com/bigdataviewer/bigdataviewer-core/tree/master/src/test/java/bdv/util).
+
+## Usage
+
+```
+Random random = new Random();
+Img<ARGBType> img = ArrayImgs.argbs(100, 100, 100);
+img.forEach(t -> t.set(random.nextInt()));
+Bdv bdv = BdvFunctions.show(img, "img");
+```
+creates a random 3D ARGB img and shows it in a BDV window.
+
+All `BdvFunctions` methods will return some instance of `Bdv` which can be used to close the BDV window:
+```
+bdv.close()
+```
+or add more stuff to the same window:
+```
+BdvFunctions.show(img2, "img2", Bdv.options().addTo(bdv));
+```
+Via `bdv.getBdvHandle()` you can get access to the BDV `ViewerPanel` and `SetupAssignments` allowing more fine-grained
+manipulations of BDV state.
+
+The concrete `Bdv` instance returned from `BdvFunctions.show(img, "img")` in the above example is `BdvStackSource<ARGBType>` and
+has additional methods, e.g., `removeFromBdv()` which removes `img` from the BDV window.
+
+To display a 2D image, display a 3D image as a stack of 2D slices over time etc:
+```
+BdvFunctions.show(img2, "img2", Bdv.options().is2D());
+```
+The `is2D()` option is per Viewer window, not per stack. If it is set, the BDV navigation mouse and keybindings are set up for 2D, etc...
+
+More fine-grained control can be achieved with `axisOrder()` option:
+```
+BdvFunctions.show(img2, "img2", Bdv.options().is2D().axisOrder(XYT))
+```
+`AxisOrder` specifies how the stack dimensions are interpreted.
+For BDV with 3D navigation, the follwoing are useful: `XYZ, XYZC, XYZT, XYZCT, XYZTC`.
+For BDV with 2D navigation, the following are useful: `XY, XYC, XYT, XYCT, XYTC`.
+You should interpret `C` and `T` losely. The effect is that `T` will be mapped to the time slider of the BDV,
+while `C` is mapped to BDV sources.
+(This also means that you should not have images with a large `C` dimension.)
+
+There is/will be stuff to add annotation overlays. Currently `BdvFunctions.showPoints()` is available.
+
+Here is an example screenshot where several 3D stacks, a set of boundary points, and 3D ellipsoids fitted to the boundary points were added to a BDV window. It also shows how the usual BDV dialogs can be used to adjust visibility / brightness / colors of tbe individual sources.
+![screenshot](../bigdataviewer-core/screenshot.png)