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---
license: apache-2.0
---
<img src="pixcell_256_cell_controlnet_banner.png" alt="pixcell_256_cell_controlnet_banner" width="500"/>
# PixCell: A generative foundation model for digital histopathology images
[[📄 arXiv]](https://arxiv.org/abs/2506.05127)[[🔬 PixCell-1024]](https://huggingface.co/StonyBrook-CVLab/PixCell-1024) [[🔬 PixCell-256]](https://huggingface.co/StonyBrook-CVLab/PixCell-256) [[🔬 Pixcell-256-Cell-ControlNet]](https://huggingface.co/StonyBrook-CVLab/PixCell-256-Cell-ControlNet) [[💾 Synthetic SBU-1M]](https://huggingface.co/datasets/StonyBrook-CVLab/Synthetic-SBU-1M)
### Load PixCell-256-Cell-ControlNet model
```python
import torch
from diffusers import DiffusionPipeline
from diffusers import AutoencoderKL
device = torch.device('cuda')
# We do not host the weights of the SD3 VAE -- load it from StabilityAI
sd3_vae = AutoencoderKL.from_pretrained("stabilityai/stable-diffusion-3.5-large", subfolder="vae")
pipeline = DiffusionPipeline.from_pretrained(
"StonyBrook-CVLab/PixCell-256-Cell-ControlNet",
vae=sd3_vae,
custom_pipeline="StonyBrook-CVLab/PixCell-pipeline-ControlNet",
trust_remote_code=True,
)
pipeline.to(device);
```
### Load [[UNI-2h]](https://huggingface.co/MahmoodLab/UNI2-h) for conditioning
```python
import timm
from timm.data import resolve_data_config
from timm.data.transforms_factory import create_transform
timm_kwargs = {
'img_size': 224,
'patch_size': 14,
'depth': 24,
'num_heads': 24,
'init_values': 1e-5,
'embed_dim': 1536,
'mlp_ratio': 2.66667*2,
'num_classes': 0,
'no_embed_class': True,
'mlp_layer': timm.layers.SwiGLUPacked,
'act_layer': torch.nn.SiLU,
'reg_tokens': 8,
'dynamic_img_size': True
}
uni_model = timm.create_model("hf-hub:MahmoodLab/UNI2-h", pretrained=True, **timm_kwargs)
uni_transforms = create_transform(**resolve_data_config(uni_model.pretrained_cfg, model=uni_model))
uni_model.eval()
uni_model.to(device);
```
### Mask-conditioned generation
```python
# Load image
import numpy as np
from PIL import Image
from huggingface_hub import hf_hub_download
# This is an example image/mask pair we provide
image_path = hf_hub_download(repo_id="StonyBrook-CVLab/PixCell-256-Cell-ControlNet", filename="test_image.png")
mask_path = hf_hub_download(repo_id="StonyBrook-CVLab/PixCell-256-Cell-ControlNet", filename="test_mask.png")
image = Image.open(image_path).convert("RGB")
mask = np.asarray(Image.open(mask_path).convert("RGB"))
# Extract UNI embedding from the image
uni_inp = uni_transforms(image).unsqueeze(dim=0)
with torch.inference_mode():
uni_emb = uni_model(uni_inp.to(device))
# reshape UNI to (bs, 1, D)
uni_emb = uni_emb.unsqueeze(1)
print("Extracted UNI:", uni_emb.shape)
# Get unconditional embedding for classifier-free guidance
uncond = pipeline.get_unconditional_embedding(uni_emb.shape[0])
# Generate new samples using the given mask
samples = pipeline(uni_embeds=uni_emb, controlnet_input=mask, negative_uni_embeds=uncond, guidance_scale=2.5, num_images_per_prompt=1).images
``` |