/cellpose-cell-segmentation

name: "cellpose-cell-segmentation"
description: "DL cell/nucleus segmentation for fluorescence and brightfield microscopy. Pre-trained models (cyto3, nuclei, tissuenet) and a generalist flow-based algorithm segment cells without retraining. Outputs label masks for morphology and tracking. Use scikit-image watershed for rule-based; Cellpose when DL generalization across staining is needed."
license: "BSD-3-Clause"

Cellpose — Deep Learning Cell Segmentation

Overview

Cellpose uses a flow-based neural network to segment individual cells or nuclei in fluorescence microscopy images without manual parameter tuning. Pre-trained models (`cyto3`, `nuclei`, `tissuenet`) generalize across cell types, magnifications, and staining conditions — eliminating the need for manual threshold selection or watershed parameter optimization. Cellpose outputs integer label masks (each cell = unique integer) compatible with scikit-image `regionprops` for morphology measurement and with TrackPy for tracking. A built-in diameter estimator removes the need to specify cell size, though providing an approximate diameter improves accuracy.

When to Use

• Segmenting cells or nuclei in fluorescence microscopy images where rule-based thresholding fails due to varying intensity or cell touching
• Processing large microscopy datasets in batch without per-image parameter tuning
• Segmenting diverse cell types (adherent cells, blood cells, bacteria, organoids) with a single model
• Producing label masks for downstream region property measurement (area, intensity, shape) with scikit-image
• 3D volumetric segmentation of z-stack microscopy data with `do_3D=True`
• Use **scikit-image watershed** when cells are well-separated and rule-based thresholding is sufficient
• Use **StarDist** as an alternative deep learning segmenter optimized for star-convex cells (neurons, nuclei)

Prerequisites

• **Python packages**: `cellpose`, `numpy`, `matplotlib`
• **Optional**: GPU with CUDA for 10-50× speedup (`pip install cellpose[gui]` for GUI)
• **Input**: grayscale or multichannel TIFF/PNG images (2D or 3D arrays)

# Install Cellpose
pip install cellpose

# Install with GUI support
pip install cellpose[gui]

# Install with GPU (PyTorch CUDA)
pip install cellpose torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cu118

# Verify
python -c "from cellpose import models; print('Cellpose ready')"

Quick Start

from cellpose import models
import numpy as np
from skimage import io

# Load image (grayscale or 2D array)
img = io.imread("cells.tif")  # shape: (H, W) or (H, W, C)

# Initialize model and segment
model = models.Cellpose(model_type="cyto3", gpu=False)
masks, flows, styles, diams = model.eval(img, diameter=0, channels=[0, 0])

print(f"Cells segmented: {masks.max()}")  # number of cells
print(f"Estimated diameter: {diams:.1f} px")
print(f"Mask shape: {masks.shape}")

Workflow

Step 1: Load and Inspect Images

Load microscopy images and inspect channel layout before segmentation.

import numpy as np
from skimage import io
import matplotlib.pyplot as plt

# Load single-channel fluorescence image
img_gray = io.imread("nucleus_dapi.tif")           # shape: (H, W)
img_rgb = io.imread("cells_multichannel.tif")      # shape: (H, W, C)

print(f"Grayscale shape: {img_gray.shape}, dtype: {img_gray.dtype}")
print(f"Multichannel shape: {img_rgb.shape}")

# Preview
fig, axes = plt.subplots(1, 2, figsize=(12, 5))
axes[0].imshow(img_gray, cmap="gray")
axes[0].set_title("DAPI (nuclei)")
axes[1].imshow(img_rgb[..., 0], cmap="green")
axes[1].set_title("GFP channel")
plt.tight_layout()
plt.savefig("image_preview.png", dpi=100)
print("Saved: image_preview.png")

Step 2: Segment Cells with a Pre-trained Model

Run Cellpose with the appropriate pre-trained model.

from cellpose import models
import numpy as np
from skimage import io

# Available models: 'cyto3' (cells), 'nuclei', 'tissuenet', 'cyto2', 'CP'
model = models.Cellpose(model_type="cyto3", gpu=False)

img = io.imread("cells.tif")

# channels=[cytoplasm_channel, nucleus_channel]
# Use [0, 0] for grayscale; [1, 3] for green cytoplasm + blue nucleus (1-indexed)
masks, flows, styles, diams = model.eval(
    img,
    diameter=0,          # 0 = auto-estimate; or provide px estimate
    channels=[0, 0],     # grayscale
    flow_threshold=0.4,  # lower = fewer false positives; range 0.1-1.0
    cellprob_threshold=0.0,  # lower = more cells detected; range -6 to 6
)

print(f"Cells found: {masks.max()}")
print(f"Estimated cell diameter: {diams:.1f} pixels")
np.save("masks.npy", masks)

Step 3: Segment Nuclei from DAPI Channel

Use the `nuclei` model for DAPI-stained nuclei.

from cellpose import models
from skimage import io
import numpy as np

model = models.Cellpose(model_type="nuclei", gpu=False)
dapi = io.imread("dapi.tif")

# Nucleus-only segmentation: channels=[0, 0] (single channel)
masks, flows, styles, diams = model.eval(
    dapi,
    diameter=30,         # approximate nucleus diameter in pixels
    channels=[0, 0],
    flow_threshold=0.4,
    cellprob_threshold=0.0,
)

print(f"Nuclei segmented: {masks.max()}")
# Save label mask as TIFF for ImageJ/FIJI compatibility
from skimage import io as skio
skio.imsave("nuclei_masks.tif", masks.astype(np.uint16))
print("Saved: nuclei_masks.tif")

Step 4: Visualize Segmentation Results

Overlay masks on original images for quality control.

from cellpose import plot as cpplot
import matplotlib.pyplot as plt
import numpy as np
from skimage import io

img = io.imread("cells.tif")
masks = np.load("masks.npy")
flows_data = None  # load if you saved them: flows = np.load("flows.npy", allow_pickle=True)

# Cellpose built-in visualization
fig, axes = plt.subplots(1, 3, figsize=(15, 5))

# Original image
axes[0].imshow(img, cmap="gray")
axes[0].set_title(f"Original image")

# Label mask (each cell = unique color)
axes[1].imshow