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|[Path optimization](./manual#refinefit-)| Supported |See [Re-trace With A*](./manual#re-trace-with-a)|
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| 3D Visualization: Interactive re-slicing browser | Supported via [BigDataViewer](./manual#big-data-viewer)||
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| 3D Visualization: Interactive volume viewer | Supported via [BigVolumeViewer](./manual#big-volume-viewer) and [sciview](./manual#sciview)| Includes [Slab View](#slab-view) for restricting rendering to a thin, adjustable region of the volume |
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| Stream-specific workflows | Supported (experimental) |[Materialized crops](./snt-stream#materialized-crops), [channel unmixing](./snt-stream#channel-unmixing), and [Quick Connect](./snt-stream#editing): see [SNT Stream](./snt-stream)|
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| Multidimensional operations | Limited support | Tracing handles one active channel/frame at a time for performance reasons. Commands that require exposing all channels/frames to be available at once [may not be supported](#limitations-and-idiosyncrasies)|
| Multidimensional operations | Limited support | Tracing handles one active channel/frame at a time for performance reasons. Commands that require exposing all channels/frames to be available at once may require [data crops](#limitations-and-idiosyncrasies)|
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<sup>1</sup>For collaborative tracing, please use [HortaCloud](https://hortacloud.org/): This is SNT's development team recommended tool for tracing Terabyte-size datasets in a collaborative environment
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@@ -56,7 +56,7 @@ Choose _Big Data..._ from the [Shortcuts Window](./manual#snt-commands). In the
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|**Display**| 3D volume rendering | Interactive reslicing |
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|**Hardware**| Discrete graphics card recommended | No GPU needed |
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|**[Slab View](#slab-view)**| Available | N/A |
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|**[Slab view](#slab-view)**| Available | N/A |
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|**[Channel unmixing](./snt-stream#channel-unmixing)**| Computed per slab | Live |
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Choose BVV for sparsely labeled data, modern hardware, and a fast disk or network connection. Choose BDV for dense, feature-rich images, modest hardware, or slow connections.
@@ -65,14 +65,14 @@ Choose _Big Data..._ from the [Shortcuts Window](./manual#snt-commands). In the
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-**Load Remote Demo**: Pre-fills all fields with a remote demo (marmoset neurons, OME-Zarr, with autotracings and soma markers, using BVV with tracing enabled)
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All inputs can be local paths or remote URLs (including http and s3 links). Only _Main volume_ is mandatory.
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{% include notice icon="info" content="**[SNT Stream](./snt-stream) remains experimental**." %}
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{% include notice icon="info" content="**All inputs can be local paths or remote URLs. Only _Main volume_ is mandatory**." %}
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## Limitations and Idiosyncrasies
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-**One channel/frame at a time**: for performance reasons, one channel/frame is streamed for tracing at once. Commands that require all channels/frames available simultaneously (e.g., [Multispectral Refinement](./manual#multispectral-refinement)) are not supported
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-**One channel/frame at a time**: for performance reasons, one channel/frame is streamed for tracing at once. Commands that require all channels/frames available simultaneously (e.g., [Multispectral Refinement](./manual#multispectral-refinement)) require [materialized regions](./manual#materialize-regions).
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-**Fixed search algorithm**: the A* search algorithm is used for interactive tracing; the alternate NBA*/Fast Marching options available for in-core images may not be offered in Stream mode
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-**Cached image statistics**: Access to cost-function tuning and [image-statistics options](./manual#algorithm-settings) remains available. However, since _Compute Now For Whole Image_ scans the entire streamed dataset once, it can be _slow_ depending on dataset size and network/disk speed. Use _Compute Real-Time_ (the default) instead: It recalculates local statistics as you trace new regions.
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-**3D Scene recentering on click**: whether/how the view recenters as you place tracing points is configurable from the toolbar's options menu (_Never_ / _Adaptive_ / _Always_). _Adaptive_ is the recommended default for streamed data: it skips recentering for clicks that already land close to the focal plane, and briefly gates subsequent clicks after a recenter fires, giving tile streaming time to catch up
@@ -96,13 +96,13 @@ Slab View switches itself off if the view no longer intersects the slab, and whe
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[Big volume viewer](./manual#big-volume-viewer) and [Big data viewer](./manual#big-data-viewer) are at the core of Big-data support. Standard formats (TIFF, and anything readable via [Bio-Formats](/formats/bio-formats)) are loaded as regular in-memory volumes, with an option to downsample automatically if a volume exceeds the GPU's 3D texture limits.
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Imaris (.ims) files are supported via an automatically generated BDV-XML sidecar written next to the original file.
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For genuinely large datasets, BDV XML/HDF5, N5, and OME-Zarr/OME-NGFF containers are opened virtually: data is streamed from disk in blocks as needed. N5 and Zarr containers are read directly, with no XML sidecar required. Remote data can be also be loaded using URLs.
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For genuinely large datasets, BDV XML/HDF5, N5, and OME-Zarr containers are opened virtually: data is streamed from disk in blocks as needed. N5 and Zarr containers are read directly, with no XML sidecar required. Remote data can be also be loaded using URLs.
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### Non-pyramidal and oversized volumes
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### Non-pyramidal and Oversized Volumes
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BVV's 3D renderer requires a multi-resolution pyramid, and a single GPU texture has size limits. If the _Main volume_ does not satisfy these and BVV is chosen, SNT prompts you for how to proceed:
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-**Non-pyramidal N5/Zarr**: Choose _Build Pyramid_ to have SNT compute the coarser levels on demand (volumes that fit in memory are first copied locally, which may take a while for remote datasets)
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-**Non-pyramidal Zarr/N5**: Choose _Build Pyramid_ to have SNT compute the coarser levels on demand (volumes that fit in memory are first copied locally, which may take a while for remote datasets)
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-**Image too large for a single GPU texture**: This happens when a dimension exceeds the 3D texture limit of your graphics card, or when the volume has too many voxels per channel. You can choose between:
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-_Downsample_: Shrinks the image so that it fits. Opens quickly, but fine detail is lost
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-_Load at full resolution_: Loads every voxel into memory as a tiled pyramid. Requires substantial memory, and is a rendering only: it cannot be used for tracing
Copy file name to clipboardExpand all lines: _pages/plugins/snt/key-shortcuts.md
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@@ -13,7 +13,7 @@ update-site: Neuroanatomy
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{% include snt-modes %}
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{% capture version%}
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**This page was last revised for [version 5.0.13](https://github.com/morphonets/SNT/releases)**.
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**This page was last revised for [version 5.0.21](https://github.com/morphonets/SNT/releases)**.
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{% endcapture %}
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{% include notice icon="snt" content=version %}
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@@ -32,13 +32,12 @@ The [Command Palette](manual#command-palette) ({% include key keys='ctlcmd|Shift
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{% capture legend %}
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Unless marked, shortcuts work in all tracing canvases: the classic XY/ZY/XZ views and [SNT Stream](./snt-stream) (BDV/BVV). Marked shortcuts are limited to one of them:
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|{{ crop }} | Requires an image loaded as an ImagePlus: the classic canvas, or a _materialized crop_ in [Stream Mode](./snt-stream)|
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|{{ stream }} |Stream Mode only|
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{{ crop }} → Requires an image fully loaded into memory: A traditional image or a [materialized regions](./manual#materialized-regions) in Stream mode<br>
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{{ stream }} → Stream Mode only
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In Stream Mode, BDV/BVV's own shortcuts are retained unless noted otherwise. The full list of active shortcuts can be accessed from the options drop-down menu of the _Scene Controls_ widget of BDV/BVV.
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The [Legacy 3D Viewer](#legacy-3d-viewer) does not support most of the shortcuts listed here.
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In Stream Mode, BDV/BVV's own shortcuts are retained unless noted otherwise.
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{% endcapture %}
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{% include notice icon="info" content=legend %}
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{% include notice icon="snt-stream" content=legend %}
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