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README.md
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@@ -29,7 +29,7 @@ Checkpoints behind the [CELL-FM CondenSeq demo](https://huggingface.co/spaces/Bo
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| `opencell/vit.bin` | The same ViT fine-tuned on OpenCell, 1,311 classes. Identical backbone to `hpa/vit.bin`, but its input stem takes **two** channels — protein and nucleus — where the HPA one takes four, so the two cannot be swapped: the count is fixed in `conv_proj` and a mismatch fails there | `finetune_opencell/vit/checkpoint-10000` |
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| `opencell/vs_anchor_nucleus.npy` | The nucleus every OpenCell generation is conditioned on: `(1, 256, 256)` float32 in [-1, 1]. Gene ATG7, crop `CID001813_FID00035838_proj_11` — bit-for-bit the conditioning channel of the published offline run | built |
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| `opencell/vs_genes.csv` | OpenCell's 1,311 genes: name, protein name, UniProt accession, Ensembl id, localization annotation and sequence. The metadata table minus its image paths | built |
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| `opencell/vs_reference_cells.npz` | Four proteins in two matched pairs (POLR1A/SNRPF nuclear, LSM14A/DDX6 both P-body), each with
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| `hpa/anchor_cell.npy` | The fixed cell every NLS-screening image is conditioned on: `(3, 256, 256)` float32 in [-1, 1], channels nucleus, ER, microtubules. HPA gene H3C13, cell crop `1194_B2_2_4` | built |
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| `hpa/anchor_masks.npz` | Two 256x256 boolean masks over that cell, `nucleus` and `cell`; cytoplasm is `cell & ~nucleus` | built |
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| `hpa/pls_anchor_nls.npz` | The cell PLS generation conditions on for nuclear signals: `cell` `(3, 512, 512)` nucleus/ER/microtubules and `protein` `(1, 512, 512)`, float32 in [-1, 1]. HPA gene PPM1G (Nucleoplasm), crop `392_B9_1_11` | built |
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| `opencell/vit.bin` | The same ViT fine-tuned on OpenCell, 1,311 classes. Identical backbone to `hpa/vit.bin`, but its input stem takes **two** channels — protein and nucleus — where the HPA one takes four, so the two cannot be swapped: the count is fixed in `conv_proj` and a mismatch fails there | `finetune_opencell/vit/checkpoint-10000` |
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| `opencell/vs_anchor_nucleus.npy` | The nucleus every OpenCell generation is conditioned on: `(1, 256, 256)` float32 in [-1, 1]. Gene ATG7, crop `CID001813_FID00035838_proj_11` — bit-for-bit the conditioning channel of the published offline run | built |
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| `opencell/vs_genes.csv` | OpenCell's 1,311 genes: name, protein name, UniProt accession, Ensembl id, localization annotation and sequence. The metadata table minus its image paths | built |
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| `opencell/vs_reference_cells.npz` | Four proteins in two matched pairs (POLR1A/SNRPF nuclear, LSM14A/DDX6 both P-body), each with one real OpenCell crop as a `(nucleus, protein)` float16 pair — the image shown beside the generated one | built |
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| `hpa/anchor_cell.npy` | The fixed cell every NLS-screening image is conditioned on: `(3, 256, 256)` float32 in [-1, 1], channels nucleus, ER, microtubules. HPA gene H3C13, cell crop `1194_B2_2_4` | built |
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| `hpa/anchor_masks.npz` | Two 256x256 boolean masks over that cell, `nucleus` and `cell`; cytoplasm is `cell & ~nucleus` | built |
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| `hpa/pls_anchor_nls.npz` | The cell PLS generation conditions on for nuclear signals: `cell` `(3, 512, 512)` nucleus/ER/microtubules and `protein` `(1, 512, 512)`, float32 in [-1, 1]. HPA gene PPM1G (Nucleoplasm), crop `392_B9_1_11` | built |
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