From 0cb26cb686ebd0fe3e81d047eebe3a389abedc53 Mon Sep 17 00:00:00 2001 From: Tiago Ferreira Date: Thu, 29 Oct 2026 22:15:04 -0400 Subject: [PATCH] describe snt links and fix erroneous metric descripiton --- _pages/plugins/snt/metrics.md | 2 +- _pages/plugins/snt/snt-stream.md | 1 + _pages/plugins/snt/walkthroughs.md | 40 ++++++++++++++++++++++++++++++ 3 files changed, 42 insertions(+), 1 deletion(-) diff --git a/_pages/plugins/snt/metrics.md b/_pages/plugins/snt/metrics.md index d902d33278..45c4bbfc17 100644 --- a/_pages/plugins/snt/metrics.md +++ b/_pages/plugins/snt/metrics.md @@ -98,7 +98,7 @@ The ratio between $$area^3/volume^2$$ of the 3D [convex hull](#convex-hull), nor Defined as $$\sqrt{1 - \left(\frac{b}{a}\right)^2}$$, where $$a$$ and $$b$$ are the semi-major and semi-minor axes of the 2D [convex hull](#convex-hull). Not applicable to 3D Convex hulls. An eccentricity of 0 corresponds to a perfect circle. An eccentricity close to 1 indicates a highly elongated ellipse. Unitless ###### Convex hull: Elongation -The [caliper (Feret) diameter](https://en.wikipedia.org/wiki/Feret_diameter) of the [convex hull](#convex-hull) +How stretched the [convex hull](#convex-hull) is, defined as $$1 - \frac{b}{a}$$. In 2D, $$a$$ and $$b$$ are the longer and shorter sides of the minimum-area bounding rectangle of the polygon. In 3D, they are the longest and second-longest semi-axes of the ellipsoid with the same second moments (inertia tensor) as the polyhedron. Range of values: 0 (e.g., a circle or a sphere) to 1 (increasingly rod-like). Unitless ###### Convex hull: Roundness The extent to which the [convex hull](#convex-hull) approaches a circle (i.e., circularity in 2D) or a sphere (i.e., sphericity in 3D). Range of values: 0--1 (unitless) diff --git a/_pages/plugins/snt/snt-stream.md b/_pages/plugins/snt/snt-stream.md index 535fbe2b7f..26e53880eb 100644 --- a/_pages/plugins/snt/snt-stream.md +++ b/_pages/plugins/snt/snt-stream.md @@ -207,4 +207,5 @@ several times: results on remote data vary with network conditions. ## See Also - [Big Data](./big-data): Loading data, supported file formats, BVV vs BDV, Slab View, and current limitations +- [SNT Links](walkthroughs#creating-snt-links): Shareable links that open (and fly to a location in) streamed datasets - [Key Shortcuts](./key-shortcuts): Shortcuts for both traditional and streamed canvases diff --git a/_pages/plugins/snt/walkthroughs.md b/_pages/plugins/snt/walkthroughs.md index b8fe8e177d..4097f31e6b 100644 --- a/_pages/plugins/snt/walkthroughs.md +++ b/_pages/plugins/snt/walkthroughs.md @@ -474,3 +474,43 @@ Multispectral Refinement and standard [Fitting](/plugins/snt/manual#refinefit) s # Detecting Crossovers Described in [Curation](curation#detecting-crossovers). + + +# Creating snt:// links + +SNT links are URLs that open SNT with specific data, optionally flying to a location of interest. They can be shared in manuscripts, bug reports, tutorials or forum posts: Clicking on one opens the data in the recipient's Fiji. + +{% include notice icon="info" content="Links require a Fiji installation with an up-to-date _Neuroanatomy_ update site. If a link is opened by an installation that does not support it, an error is displayed. If you have several Fiji installations, the operating system decides which one receives the link." %} + +## Generating Links + +In SNT Stream and in standalone Big Data/Big Volume viewers, right-click a bookmark in the [Bookmark Manager](./manual#bookmarks-tab) and choose _Copy Link to Location_. For more granular control over links use the _Create SNT Link_ [template script](./scripting#bundled-templates). + +{% include notice icon="note" content=" `snt://` works well on Windows and Linux but not on macOS. `fiji://snt/` links work on all platforms." %} + +## Examples + +[fiji://snt/demo?id=4](fiji://snt/demo?id=4) + +: Loads _Drosophila OP Neuron (Complete 3D Dataset)_: Demo 4 of the demo prompt, including any demo-specific setup + +[fiji://snt/open?image=demo:OP1&tracings=demo:OP1](fiji://snt/open?image=demo:OP1&tracings=demo:OP1) + +: Loads the same demo but using image and reconstruction labels + +[fiji://snt/open?image=https%3A%2F%2Fome-zarr-scivis.s3.us-east-1.amazonaws.com%2Fv0.5%2F96x2%2Fmarmoset_neurons.ome.zarr&viewer=bvv&view=82.880,-238.968,-65.067,1](fiji://snt/open?image=https%3A%2F%2Fome-zarr-scivis.s3.us-east-1.amazonaws.com%2Fv0.5%2F96x2%2Fmarmoset_neurons.ome.zarr&viewer=bvv&view=82.880,-238.968,-65.067,1) + +: Opens a remote OME-Zarr in [SNT Stream](./snt-stream) (BVV), and flies to the specified location (`x,y,z` in world coordinates, followed by an optional timepoint. + +[fiji://snt/fly?view=82.880,-238.968,-65.067](fiji://snt/fly?view=82.880,-238.968,-65.067) + +: Zooms to the specified location on the dataset already open + + +## Format + +``` +fiji://snt/?=&= +``` + +Values must be percent-encoded (e.g., `https%3A%2F%2F...` for a URL). Images and reconstructions can be remote URLs, or local paths/`file:` URIs. Links to local files only work on the machine that has them.