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README.md

@@ -20,10 +20,12 @@ Checkpoints behind the [CELL-FM CondenSeq demo](https://huggingface.co/spaces/Bo
 | `condenseq/vit_cls.bin` | ViT condensed/diffuse classifier, 2-channel 160x160 input | `PT_CondenSeq_img_ViT_cls_R1/checkpoint-10000` |
 | `hpa/cellfm_seq2img.bin` | CELL-FM virtual-staining generator for HPA, 256x256, 3-channel conditioning (includes the ESM-C 600M encoder) | `pretrain_hpa/cellfm_seq2img/checkpoint-50000` |
 | `hpa/vae.bin` | Image VAE at 256x256, the one `hpa/cellfm_seq2img.bin` was trained against | `pretrain_hpa/vae/checkpoint-50000` |
+| `hpa/vit.bin` | Image-embedding ViT for HPA: 12 layers, 512 hidden, 2048 MLP, 8 heads, patch 4, 256x256 input. Trained to identify the protein in an image over 13,908 classes; the embedding is the representation, not the prediction. Four input channels — protein, nucleus, ER, microtubules | `pretrain_hpa/vit/checkpoint-16000` |
 | `hpa/cellfm_img2seq.bin` | CELL-FM image-to-sequence model for HPA, 512x512, 3-channel conditioning (includes the ESM-C 600M encoder) | `pretrain_hpa/cellfm_img2seq/checkpoint-60000` |
 | `hpa/vae_512.bin` | Image VAE at 512x512, the one `hpa/cellfm_img2seq.bin` was trained against — a different model from `hpa/vae.bin`, not a rename | `pretrain_hpa/vae_512/checkpoint-50000` |
 | `opencell/cellfm_vs.bin` | CELL-FM virtual-staining generator for OpenCell, 256x256, single nucleus conditioning channel, fine-tuned (includes the ESM-C 600M encoder) | `finetune_opencell/cellfm_vs/checkpoint-100000` |
 | `opencell/vae.bin` | Image VAE at 256x256, the one `opencell/cellfm_vs.bin` was trained against — OpenCell-finetuned, so not interchangeable with `hpa/vae.bin` despite the matching shape | `finetune_opencell/vae/checkpoint-50000` |
+| `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` |
 | `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 |
 | `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 |
 | `opencell/vs_reference_cells.npz` | 17 genes spanning distinct compartments, each with its own nucleus and its real protein image, float16 — the ground truth the notebook's generations are shown against | built |