MorphEm

Model Details

Model Description

MorphEm is a self supervised learning framework trained with the DINO Bag of Channels recipe on the entire CHAMMI-75 dataset. It serves as a benchmark for performance for self-supervised models.

• Developed by: Vidit Agrawal, John Peters, Juan Caicedo
• Shared by: Caicedo Lab
• Model type: Vision Transformer Small
• License: MIT License

Model Sources

• Repository: https://github.com/CaicedoLab/CHAMMI-75

• Demo: https://github.com/CaicedoLab/CHAMMI-75/tree/main/aws-tutorials

Uses

The model was pre-trained with a heterogenous dataset of microscopy images with the goal of obtaining cell morphology embeddings for biological applications.

Direct Use

The primary use of this model is feature extraction of cellular morphology in image-based biological experiments. The model takes single-channel images as input and produces feature vectors with discriminative information of cellular phenotypes. The input images should be segmented ahead of time; this model does not identify the location of cells automatically. The feature embeddings have been tested in single-cell analysis problems. If the images of interest are multi-channel, each channel can be processed independently and then the feature embeddings of all channels are concatenated for downstream applications. The applications of the embeddings produced by this model include basic biology research, functional genomics studies, drug discovery projects, among others.

Out-of-Scope Use

This model is not useful for cell segmentation, its primary use is feature extraction only. The model should be use for analyzing imaging data in biological laboratories. It is not intented to be use in clinical practice or in diagnostic applications. The model should not be used for applications that involve biological weapons, or any other type of biological manipulation that could harm humans or the natural environment.

How to Get Started with the Model

Use the code below to get started with the model.

from transformers import AutoModel
import torch
import torch.nn as nn
import torchvision
from torchvision import transforms as v2
import numpy as np

# Noise Injector transformation
class SaturationNoiseInjector(nn.Module):
    def __init__(self, low=200, high=255):
        super().__init__()
        self.low = low
        self.high = high

    def forward(self, x: torch.Tensor) -> torch.Tensor:
        channel = x[0].clone()
        noise = torch.empty_like(channel).uniform_(self.low, self.high)
        mask = (channel == 255).float()
        noise_masked = noise * mask
        channel[channel == 255] = 0
        channel = channel + noise_masked
        x[0] = channel
        return x


# Self Normalize transformation
class PerImageNormalize(nn.Module):
    def __init__(self, eps=1e-7):
        super().__init__()
        self.eps = eps
        self.instance_norm = nn.InstanceNorm2d(
            num_features=1,
            affine=False,
            track_running_stats=False,
            eps=self.eps,
        )

    def forward(self, x: torch.Tensor) -> torch.Tensor:
        if x.dim() == 3:
            x = x.unsqueeze(0)
        x = self.instance_norm(x)
        if x.shape[0] == 1:
            x = x.squeeze(0)
        return x


# Load model
device = "cuda" if torch.cuda.is_available() else "cpu"
model = AutoModel.from_pretrained("CaicedoLab/MorphEm", trust_remote_code=True)
model.to(device).eval()

# Define transforms
transform = v2.Compose([
    SaturationNoiseInjector(),
    PerImageNormalize(),
    v2.Resize(size=(224, 224), antialias=True),
])

# Generate random batch (N, C, H, W)
batch_size = 2
num_channels = 3
images = torch.randint(0, 256, (batch_size, num_channels, 512, 512), dtype=torch.float32)

print(f"Input shape: {images.shape} (N={batch_size}, C={num_channels}, H=512, W=512)")
print()

# Bag of Channels (BoC) - process each channel independently
with torch.no_grad():
    batch_feat = []
    images = images.to(device)
    
    for c in range(images.shape[1]):
        # Extract single channel: (N, C, H, W) -> (N, H, W)
        single_channel = images[:, c, :, :]
        
        # Apply transforms, add dimension 1 ((N, 1, H, W))
        single_channel = transform(single_channel).unsqueeze(1)
        
        # Extract features
        output = model.forward_features(single_channel)
        feat_temp = output["x_norm_clstoken"].cpu().detach().numpy()
        batch_feat.append(feat_temp)

# Concatenate features from all channels
features = np.concatenate(batch_feat, axis=1)

print(f"Output shape: {features.shape}")
print(f"  - Batch size (N): {features.shape[0]}")
print(f"  - Feature dimension (C * feature_dim): {features.shape[1]}")

Training Details

Training Data

MorphEm was pre-trained on the entire CHAMMI-75 pre-training data. The CHAMMI-75 dataset consists of 75 heterogenous studies and 2.8 million multi-channel images.

Training Procedure

We have utilized the self-supervised learning framework called DINO. We pre-trained a model which inputs a single channel one at a time. For evaluation, you would concatenate each channel specifically.

Preprocessing

We used three transforms mainly for preprocessing: SaturationNoiseInjector(), SelfImageNormalize(), Resize(224,224)

# Noise Injector transformation
class SaturationNoiseInjector(nn.Module):
    def __init__(self, low=200, high=255):
        super().__init__()
        self.low = low
        self.high = high

    def forward(self, x: torch.Tensor) -> torch.Tensor:
        channel = x[0].clone()
        noise = torch.empty_like(channel).uniform_(self.low, self.high)
        mask = (channel == 255).float()
        noise_masked = noise * mask
        channel[channel == 255] = 0
        channel = channel + noise_masked
        x[0] = channel
        return x


# Self Normalize transformation
class PerImageNormalize(nn.Module):
    def __init__(self, eps=1e-7):
        super().__init__()
        self.eps = eps
        self.instance_norm = nn.InstanceNorm2d(
            num_features=1,
            affine=False,
            track_running_stats=False,
            eps=self.eps,
        )

    def forward(self, x: torch.Tensor) -> torch.Tensor:
        if x.dim() == 3:
            x = x.unsqueeze(0)
        x = self.instance_norm(x)
        if x.shape[0] == 1:
            x = x.squeeze(0)
        return x

Evaluation

We have evaluated this model on 6 different benchmarks. The model is highly competitive in most of them. The benchmarks are listed below:

1. CHAMMI
2. HPAv23
3. Jump-CP
4. IDR0017
5. CELLPHIE
6. RBC-MC

More details can be found in the paper:

Summary

Environmental Impact

• Hardware Type: Nvidia RTX A6000
• Hours used: 2352
• Cloud Provider: Private Infrastructure
• Compute Region: Private Infrastructure
• Carbon Emitted: 304 kg CO2

Technical Specifications

The model is a ViT Small trained on 2500 Nvidia A6000 GPU hours. The model was trained on a multi-node system with 2 nodes, each containing 7 GPUs.

Citation

BibTeX:

@inproceedings{
agrawal2026chammi,
title={{CHAMMI}-75: Pre-training multi-channel models with heterogeneous microscopy images},
author={Vidit Agrawal and John Peters and Tyler N. Thompson and Mohammad Vali Sanian and Chau Pham and Nikita Moshkov and Arshad Kazi and Aditya Pillai and Jack Freeman and Byunguk Kang and Samouil L. Farhi and Ernest Fraenkel and Ron M. Stewart and Lassi Paavolainen and Bryan A. Plummer and Juan C. Caicedo},
booktitle={The Fourteenth International Conference on Learning Representations},
year={2026},
url={https://openreview.net/forum?id=SLjqdj3LPk}
}

Model Card Authors

Vidit Agrawal, John Peters, Juan C. Caicedo

Model Card Contact

vagrawal22@wisc.edu, jgpeters3@wisc.edu, juan.caicedo@wisc.edu