Update README.md

README.md

@@ -25,7 +25,7 @@ Recommended defaults: **QuantEM for mitochondria; OmniEM for ER, nucleus and lip
 
 ## Use
 
-These files are not loaded directly. Install the library, which resolves, downloads, verifies and
+These files are not loaded directly. Install the core library, which resolves, downloads, verifies and
 assembles them for you:
 
 ```bash
@@ -39,32 +39,12 @@ model = load_model("quantem/mito")          # downloads on first use, then cache
 labels = segment(model, image, pixel_size_nm=8.0)
 ```
 
-For a GUI, install the napari plugin instead — it wraps the same library with segmentation,
-proofreading, head-only fine-tuning, batch mode and morphometrics:
-
-```bash
-pip install napari-quantem
-```
-
-Pre-seed a shared or air-gapped cache with:
-
-```bash
-python -m quantem_em.weights download --all
-QUANTEM_MODEL_DIR=/srv/quantem python -m quantem_em.weights verify
-```
+For a GUI, install the napari plugin or the application instead — they incorporate segmentation, fine-tuning, 
+and downstream metrics. See https://github.com/ArrojoDrigoLab/QuantEM
 
 ## Files
 
-Encoders are split so nothing is downloaded twice. **The split is not uniform**, because the
-families adapt their encoders differently:
-
-* **OmniEM** uses LoRA, which never touches the base weights — so `omniem-vitl` is a complete
-  encoder genuinely shared by all four heads, and each head is only ~26 MB.
-* **QuantEM** mito/nucleus/LD fine-tune the **last four blocks**, which therefore differ per
-  organelle. `quantem-vitb-trunk` is blocks 0–7 plus embeddings and the final norm; blocks 8–11
-  ship inside each organelle file.
-* **`quantem-er` is self-contained.** It was adapted with `full`, replacing the whole encoder, so
-  it needs no trunk.
+Encoders are split to avoid inefficient duplicate weight downloads. 
 
 | File | Size | Contents | SHA-256 |
 |---|--:|---|---|
@@ -79,14 +59,13 @@ families adapt their encoders differently:
 | `omniem-ld.safetensors` | 25.7 MB | model | `ae5b0c356e0fb48d…` |
 | `omniem-er.safetensors` | 135.2 MB | model | `3e3a693ea757d500…` |
 
-Every file is verified against the SHA-256 above on download **and on every subsequent load**, so a
-truncated or altered file is detected rather than trusted.
+Every file is verified against the SHA-256 above on download.
 
 ## Licence
 
 **The weights are released under [CC BY 4.0](https://creativecommons.org/licenses/by/4.0/).**
-Commercial use, redistribution and modification are permitted; the only condition is attribution —
-credit the QuantEM authors, link to the licence, and indicate if you made changes.
+If using OmniEM-based models, you should cite its original publication in addition to ours:
+https://www.biorxiv.org/content/10.1101/2025.04.13.648639
 
 ## Attribution