Add docs for calculating structure tensor

docs/structure-tensor.md

@@ -0,0 +1,45 @@
+# Calculating Structure Tensor
+
+## Prerequisites
+
+Ensure the repository is cloned and its dependencies are installed.
+
+Steps to Calculate Structure Tensor
+
+1. Run Structure Tensor Calculation
+
+Use the process_zarr function to compute the structure tensor from your input Zarr file. Adjust sigma and rho to control the smoothing parameters:
+```
+input = "/scratch/input.zarr"
+output = "/scratch/output.zarr"
+process_zarr(input, output, sigma=0, rho=5)
+```
+	•	sigma: Controls the Gaussian smoothing applied before computing derivatives.
+	•	rho: Controls the Gaussian smoothing applied after computing the tensor.
+
+2. Generate Pyramid for Multi-Resolution Data
+
+To enable visualization or efficient access, create a resolution pyramid with generate_pyramid:
+`
+generate_pyramid(Zarr.zopen(output, "w"), levels=6, mode="mean")
+
+	•	levels: Specifies the number of pyramid levels.
+	•	mode: Determines the aggregation method (e.g., mean).
+`
+3. Add OME Metadata
+
+To make the output Zarr file compatible with tools like Neuroglancer or Napari, write OME-compliant metadata:
+`
+write_ome_metadata(Zarr.zopen(output, "w"), ["c", "z", "y", "x"])
+
+	•	Dimensions: ["c", "z", "y", "x"] corresponds to the channel, depth, height, and width dimensions of the data.
+`
+Example Workflow
+	1.	Input: /scratch/input.zarr
+	2.	Output: /scratch/output.zarr
+`
+process_zarr("/scratch/input.zarr", "/scratch/output.zarr", sigma=0, rho=5)
+generate_pyramid(Zarr.zopen("/scratch/output.zarr", "w"), levels=6, mode="mean")
+write_ome_metadata(Zarr.zopen("/scratch/output.zarr", "w"), ["c", "z", "y", "x"])
+`
+This pipeline will produce a multi-resolution Zarr dataset ready for visualization and further analysis.

mkdocs.yml

@@ -22,6 +22,7 @@ nav:
   - Welcome: "index.md"
   - Upload data: "upload.md"
   - Visualize data in Neuroglancer: "neuroglancer.md"
+  - Calculating Structure Tensor: "structure-tensor.md"
   - Webknossos:
     - Add Webknossos dataset: "webknossos-add-dataset.md"
     - Deployment: https://github.com/lincbrain/webknossos/blob/ak-dev/LINC_DEPLOYMENT.md