Historical documentation for deprecated tools, workflows, and procedures. Preserved for institutional memory and reference.
Historical Reference Only. The tools and workflows documented here have been superseded by modern alternatives. See Pipeline and Tasks for current procedures.
Desktop application for manual segmentation annotation. Required Ubuntu/Linux environment with network-mounted storage.
3D proofreading and visualization tool for segmentation data. Desktop application for reviewing and correcting automated segmentation.
Browser-based citizen science game for neuron reconstruction. Gamified approach to crowdsourced annotation.
Original annotation workflow using desktop applications on Ubuntu workstations with network-mounted data storage.
Manual tracking of segment IDs in spreadsheets without automated validation against changing segmentation.
Terms from deprecated tools that may appear in legacy documentation. Some terms remain in use.
| Dust | Small voxel fragments erroneously included inside large dendrites or axons. Typically noise from segmentation. |
|---|---|
| Merger | AI segmentation error where two non-connecting structures are incorrectly combined into one segment. |
| Split | AI segmentation error where one continuous structure is incorrectly divided into multiple segments. |
| Segment | A collection of supervoxels grouped together, representing a candidate neuron or fragment. |
| Supervoxel | The smallest rearrangeable unit of segmentation. Groups of voxels that are always kept together. |
| Spine | Small membranous protrusion from a dendrite, typically a postsynaptic structure. |
| Volume | A 3D EM image stack loaded for annotation. |
|---|---|
| Brush | Tool for painting segmentation labels onto voxels. |
| Label | A semantic category assigned to segmented regions (e.g., "synapse", "mitochondria"). |
The original monolithic documentation page has been preserved in its entirety.
Standard Operating Procedures that have been superseded by current versions.
Original Google Docs exports preserved for reference.