Skip to content

Commit 92aa1c3

Browse files
committed
Update Neuroglancer documentation and add example
1 parent e9c25a0 commit 92aa1c3

File tree

2 files changed

+13
-2
lines changed

2 files changed

+13
-2
lines changed
Loading

docs/neuroglancer.md

Lines changed: 13 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
# Using Neuroglancer to Visualize Structure Tensors in Zarr Format
1+
# Using Neuroglancer to Visualize Orientation Vector in Zarr Format
22

33
## 1. Ensure the vector dimension is in a single chunk
44

@@ -8,10 +8,14 @@ Neuroglancer requires that the dimension along the channels (where your vector d
88

99
Once you have your data chunked correctly, you can load the Zarr dataset into Neuroglancer. Typically, you will:
1010

11-
1. Start Neuroglancer (either locally or on a server).
11+
## 2.1 Start Local Neuroglancer Server
12+
1. Start Neuroglancer.
1213
2. Open Neuroglancer in a browser.
1314
3. Load Zarr if it presents locally `load zarr:///example.path.zarr`
1415

16+
## 2.2 Start Neuroglancer on lincbrain
17+
1. Find the dataset you want to visualize
18+
2. Under `Open With` button, select Neuroglancer
1519

1620
## 3. Rename the channel dimension from `c'` to `c^`
1721

@@ -68,3 +72,10 @@ void main() {
6872
```
6973

7074
In Neuroglancer, you can paste this shader code in the layer’s Shader Editor (usually found under the “Layer” panel).
75+
76+
77+
## 5. Example
78+
79+
An example dataset can be found at [here](https://lincbrain.org/dandiset/000010/draft/files?location=sourcedata%2Fderivatives&page=2). The file `sample18_st_filtered.ome.zarr`. Once we change the dimension name to `c^` and apply the shader. We can see the result as following.
80+
![](img/neuroglancer_orientation_vector_example.jpeg)
81+

0 commit comments

Comments
 (0)