segtme-uni2

SegTME — Tumor Microenvironment segmentation using the UNI2 pathology foundation model with a dual-head UperNet + HoverNet-style decoder.

The model simultaneously predicts:

• Semantic segmentation — 6-class tissue map (background, neoplastic, inflammatory, connective, dead, epithelial)
• HV maps — horizontal/vertical nuclear distance gradients for instance segmentation via watershed post-processing

Architecture and model weights are separate: weights are publicly hosted on HuggingFace; the architecture is distributed as this compiled package (code not exposed).

Available Models

All three models share the same architecture and hyperparameters; only training data and checkpoint weights differ.

Architecture

Input (B, 3, 224, 224) — ImageNet-normalised
       │
       ▼
UNI2 ViT-Giant backbone (depth=24, heads=24, embed_dim=1536, patch=14)
  Multi-scale features extracted at layers 5 / 11 / 17 / 23
  Projected to 256 / 512 / 1024 / 2048 channels via Conv2d
       │
       ├──► UperNet decoder → semantic logits (B, 6, H, W)
       │
       └──► UperNet decoder → HV maps       (B, 2, H, W)

UNI2 backbone — vit_giant_patch14_224 (timm), loaded from MahmoodLab/UNI2-h pretrained weights, 1.1 B parameters.

UNI2UperHoVer — dual-head UperNet decoder; semantic head classifies tissue type per pixel; HV head produces horizontal/vertical nuclear centroid distance fields used for marker-controlled watershed instance segmentation.

Installation

pip install segtme-uni2

Dependencies installed automatically: torch, transformers, timm, safetensors, huggingface_hub.

Usage

from segtme import UNI2UperHoVer

# Load from HuggingFace (downloads weights automatically)
model = UNI2UperHoVer.from_pretrained("mizjaggy18/SegTME-UNI2-UperHoVer_TCGA-UT-0")
model.eval().cuda()

# Forward pass — input: (B, 3, H, W), ImageNet normalised, recommended 224×224 tiles
import torch
pixel_values = torch.randn(1, 3, 224, 224).cuda()
sem_logits, hv_maps = model(pixel_values)

# sem_logits: (B, 6, H, W)  — per-class tissue logits
# hv_maps:    (B, 2, H, W)  — horizontal / vertical distance gradients

Output classes

Recommended inference scale

Resize input tiles so one pixel corresponds to the target MPP before running inference:

Tiled WSI inference (example)

import torch
import torch.nn.functional as F
from torchvision.transforms.functional import normalize
from segtme import UNI2UperHoVer

model = UNI2UperHoVer.from_pretrained("mizjaggy18/SegTME-UNI2-UperHoVer_TCGA-UT-0")
model.eval().cuda()

MEAN = [0.485, 0.456, 0.406]
STD  = [0.229, 0.224, 0.225]
TILE = 224
STRIDE = 112
TARGET_MPP = 0.314

def infer_patch(patch_rgb_uint8, image_mpp):
    scale = image_mpp / TARGET_MPP
    h, w = patch_rgb_uint8.shape[:2]
    new_h, new_w = int(h / scale), int(w / scale)

    x = torch.from_numpy(patch_rgb_uint8).permute(2, 0, 1).float() / 255.0
    x = F.interpolate(x.unsqueeze(0), (new_h, new_w), mode="bilinear")
    x = normalize(x.squeeze(0), MEAN, STD).unsqueeze(0).cuda()

    with torch.no_grad():
        sem_logits, hv_maps = model(x)

    sem_pred = sem_logits.argmax(1).squeeze().cpu().numpy()   # (H, W) class indices
    hv       = hv_maps.squeeze().cpu().numpy()                # (2, H, W)
    return sem_pred, hv

Training Curriculum

Three-stage curriculum training, each stage initialised fresh (no weight inheritance):

All stages: initial LR 5×10⁻⁵, linear decay, AdamW optimiser. Backbone: UNI2-h (frozen or fine-tuned depending on stage).

Citation

If you use this model in your work, please cite:

@article{wanahmad2026segtme,
  title={SegTME-UNI2: A Foundation Model-Based Framework for Generalisable Multiclass Cell Segmentation and LLM-Driven Tumour Microenvironment Characterisation in Histopathology},
  author={Wan Ahmad, Wan Siti Halimatul Munirah and Samidi, Faris Syahmi and Ahmmed, Mohammad Badal and Thiviyanathan, Vimal Angela and Thavaraj, Selvam James and Abdul Majeed, Anwar P.P.},
  journal={arXiv preprint arXiv:2606.17702},
  year={2026},
  doi={10.48550/arXiv.2606.17702}
}

Links

• Paper (arXiv): https://arxiv.org/abs/2606.17702
• PyPI: https://pypi.org/project/segtme-uni2/
• HuggingFace (M1): https://huggingface.co/mizjaggy18/SegTME-UNI2-UperHoVer_PanNuke
• HuggingFace (M2): https://huggingface.co/mizjaggy18/SegTME-UNI2-UperHoVer_TCGA-UT-0
• HuggingFace (M3): https://huggingface.co/mizjaggy18/SegTME-UNI2-UperHoVer_TCGA-UT-012345
• UNI2 backbone: https://huggingface.co/MahmoodLab/UNI2-h