| # `segclr_inputs/` — staging JSONs for SegCLR lookup |
| |
| Per-token info for **MERGER FREE** training samples, formatted so a |
| SegCLR maintainer can pull one embedding per token without needing |
| to touch the raw NPZ training data. |
| |
| ## Files |
| |
| | File | n_samples | size | type | |
| |---|---|---|---| |
| | `segclr_inputs_clean_train.json` | 41,005 | 99 MB | B-clean (single root per sample) | |
| | `segclr_inputs_merge_train.json` | 188,812 | 584 MB | A-merge (two roots per sample, per-token y_part) | |
| |
| ## Schema |
| |
| ```json |
| { |
| "kind": "B-clean" | "A-merge", |
| "n_samples": <int>, |
| "samples": [ |
| { |
| "source_npz": "...", // training-data NPZ |
| "op_id": 39183, // sample id (B) or merge op id (A) |
| "fov_center_um": [x, y, z], |
| "n_tokens": 20, |
| |
| // B-clean: single root_id at sample level |
| "root_id": 864691136176785158, |
| |
| // A-merge: two roots + post-merge proofread root |
| "root_a": 864..., |
| "root_b": 864..., |
| "proofread_root": 864..., |
| |
| "tokens": [ |
| { |
| "token_idx": 0, |
| "abs_um": [x, y, z], // absolute world coords (µm) |
| "rel_um": [x, y, z], // relative to fov_center_um |
| "root_id": 864..., // per-token root assignment |
| "sv_id": "100497...", // A-merge only: supervoxel id (uint64 → str) |
| "y_part": 1 // A-merge only: 0=root_a, 1=root_b, -1=ignore |
| }, |
| ... |
| ] |
| }, |
| ... |
| ] |
| } |
| ``` |
| |
| ## Notes for SegCLR lookup |
|
|
| - **A-merge tokens already have `sv_id`** — direct SegCLR embedding |
| lookup, no CAVE chunkedgraph resolution needed. |
| - **B-clean tokens have only `root_id` + `abs_um`** — SV resolution |
| via CAVE is required before SegCLR lookup. Happy to do this on |
| our side if it saves you time; let me know. |
| - `abs_um` is in microns (1 µm = 250 voxels in xy at 4nm, 25 voxels |
| in z at 40nm). |
| - Datastack: `minnie65_public`. |
| |
| ## Direct download |
| |
| ``` |
| https://huggingface.co/datasets/FumingY/MergeFree/resolve/main/segclr_inputs/segclr_inputs_clean_train.json |
| https://huggingface.co/datasets/FumingY/MergeFree/resolve/main/segclr_inputs/segclr_inputs_merge_train.json |
| ``` |
| |
| ## What we'd like back |
| |
| One SegCLR embedding (float32) per token, joinable back via |
| `(sample.op_id, token.token_idx)`. NPZ / parquet / per-sample JSON |
| all fine. |
| |
