|
8 | 8 |
|
9 | 9 | A viewer for ome-zarr images. |
10 | 10 |
|
| 11 | +## Single canvas viewer |
| 12 | + |
| 13 | +You can load a v0.4 or v0.5 OME-Zarr file into a single-canvas 2d/3d viewer using the `oz-viewer view` CLI. See the example below. Replace the file path with the path to your image. This works for both local and remote data. |
| 14 | + |
| 15 | +```sh |
| 16 | +oz-viewer view path/to/image.ome.zarr |
| 17 | +``` |
| 18 | + |
| 19 | +Example viewing a https://livingobjects.ebi.ac.uk/idr/zarr/v0.5/idr0066/ExpA_VIP_ASLM_on.zarr (1937, 2048, 2048), anisotropic voxels (file was on local SSD). |
| 20 | + |
| 21 | +https://github.com/user-attachments/assets/59c31e89-db42-4cec-ae4f-373d997c227f |
| 22 | + |
| 23 | +## Orthoviewer |
| 24 | + |
| 25 | +You can load a v0.4 or v0.5 OME-Zarr file into an orthoviewer using the `oz-viewer ortho ` CLI. See the example below. Replace the file path with the path to your image. This works for both local and remote data. |
| 26 | + |
| 27 | +```sh |
| 28 | +oz-viewer ortho path/to/image.ome.zarr |
| 29 | +``` |
| 30 | + |
| 31 | +Example viewing https://livingobjects.ebi.ac.uk/idr/zarr/v0.5/idr0066/ExpA_VIP_ASLM_on.zarr (1937, 2048, 2048), anisotropic voxels (file was on local SSD). |
| 32 | + |
| 33 | +https://github.com/user-attachments/assets/a6c0cab9-0cd9-4fe0-80c2-c77207b4fd77 |
| 34 | + |
| 35 | +You can click the multichannel button in the upper left-hand corner to toggle berween single/multichannel rendering. Example viewing the scikit-image cells3d (converted to ome-zarr) multichannel image |
| 36 | + |
| 37 | +https://github.com/user-attachments/assets/b6655863-b8fb-4eea-be84-eb031283494e |
| 38 | + |
| 39 | + |
| 40 | + |
| 41 | +## Test dataset latency |
| 42 | + |
| 43 | +The latency for fetching chunks greatly impacts the rendering performance of the viewer. High latency means that fetching chunks from the data store is slow and thus rendering feels slow. If the latency for fetching data from your image is high, you can offset it by increasing the lod_bias which causes the renderer to prefer loading lower resolution chunks. This reduces the aount of data that needs to be loaded, but sacrifices detail. |
| 44 | + |
| 45 | +To measure the latency, you can use the `oz-viewer ping` CLI. See the example below. Replace the path with the path to your data. You can use both URL and file paths. |
| 46 | + |
| 47 | +```sh |
| 48 | +oz-viewer ping https://livingobjects.ebi.ac.uk/idr/share/ome2024-ngff-challenge/idr0066/ExpC_TPH2_left_cerebellum.zarr |
| 49 | +``` |
| 50 | + |
| 51 | +To view the options, you can run |
| 52 | + |
| 53 | +```sh |
| 54 | +oz-viewer ping --help |
| 55 | +``` |
| 56 | + |
11 | 57 | ## Orthoviewer startup performance diagnostics |
12 | 58 |
|
13 | 59 | Use the orthoviewer performance flags to print startup timings |
|
0 commit comments