patchworks

Tiled processing of arbitrarily large images — any image, any function.

┌──────┬──────┬──────┐     fn(tile) → labels      ┌──────┬──────┬──────┐
│ tile │ tile │ tile │  ─────────────────────►    │  1   │  2   │  3   │
├──────┼──────┼──────┤                            ├──────┼──────┼──────┤
│ tile │ tile │ tile │                            │  4   │  5   │  6   │   globally
├──────┼──────┼──────┤                            ├──────┼──────┼──────┤   consistent
│ tile │ tile │ tile │                            │  7   │  8   │  9   │   labels
└──────┴──────┴──────┘                            └──────┴──────┴──────┘

patchworks splits a large image into tiles, runs any callable on each tile in parallel, and merges the results into a globally consistent label array. It handles terabyte-scale images without loading them into memory.

Installation

pip install patchworks

Optional extras:

pip install "patchworks[gpu]"       # GPU VRAM querying (nvidia-ml-py)
pip install "patchworks[distributed]" # Dask cluster + live dashboard
pip install "patchworks[cellpose]"  # Cellpose plugin (>=3.0, v3 or v4)
pip install "patchworks[cellpose3]" # Cellpose plugin, pinned to v3.x
pip install "patchworks[cellpose4]" # Cellpose plugin, pinned to v4+
pip install "patchworks[dog]"       # deconvolution + DoG plugin (pycudadecon)
pip install "patchworks[bioio]"     # convert any image format to OME-ZARR
pip install "patchworks[imaris]"    # convert Imaris .ims files to OME-ZARR
pip install "patchworks[napari]"    # interactive napari viewer plugin
pip install "patchworks[all]"       # Everything, incl. the napari viewer

bioio reads CZI/LIF/ND2/OME-TIFF/… The [bioio] extra bundles the common native readers (bioio-nd2, bioio-ome-tiff, bioio-czi, bioio-tifffile, bioio-lif) plus bioio-bioformats, the Bio-Formats catch-all reader (JVM). [imaris] adds native .ims support (HDF5, no JVM). Physical pixel calibration is read from the input and written into the OME-ZARR.

cupy is never installed automatically, unlike Cellpose's GPU support (which comes for free via PyTorch's self-contained CUDA wheels). Any use_gpu=True/dilate_gpu: true option (the dog plugin, dilate_labels) needs cupy installed separately, matching your CUDA version — e.g. pip install cupy-cuda12x. Not bundled because cupy ships one wheel per CUDA major version; a generic pin would resolve to the wrong build (or fail to resolve) depending on the machine.

Quick start — 5 lines

from patchworks import tile_process


def my_fn(tile):
    from skimage.filters import threshold_otsu
    from skimage.measure import label

    return label(tile > threshold_otsu(tile)).astype("int32")


result = tile_process("image.zarr", my_fn)

Done. result is a lazy dask array of integer labels (call .compute() for a NumPy array), same spatial shape as the input, with globally unique IDs across all tiles. By default the labels are also written into the input store at image.zarr/labels/labels/ as a multi-scale pyramid, so the image and its segmentation live in one OME-ZARR. Pass write_to="labels.zarr" to write a separate store instead.

With Cellpose

from patchworks import tile_process
from patchworks.plugins.cellpose import cellpose_fn

fn = cellpose_fn("cyto3", gpu=True, diameter=30)

tile_process(
    "image.zarr",
    fn,
    tile_shape=(1, 2048, 2048),  # one z-slice per tile
    overlap=20,  # gives boundary cells enough context
    write_to="labels.zarr",  # stream directly to disk — no RAM accumulation
    progress=True,
)

With StarDist

from stardist.models import StarDist2D
from patchworks import tile_process

model = StarDist2D.from_pretrained("2D_versatile_fluo")


def stardist_fn(tile):
    img = tile[0] if tile.ndim == 3 and tile.shape[0] == 1 else tile
    norm = img.astype("float32") / (img.max() or 1)
    labels, _ = model.predict_instances(norm)
    return labels.astype("int32")[None] if tile.ndim == 3 else labels.astype("int32")


tile_process(
    "image.zarr",
    stardist_fn,
    tile_shape=(1, 1024, 1024),
    overlap=32,
    write_to="labels.zarr",
    progress=True,
)

With any function

import numpy as np
from scipy.ndimage import gaussian_filter
from skimage.measure import label
from patchworks import tile_process


def my_custom_fn(tile: np.ndarray) -> np.ndarray:
    smoothed = gaussian_filter(tile.astype("float32"), sigma=1.5)
    binary = smoothed > smoothed.mean()
    return label(binary).astype("int32")


tile_process("image.zarr", my_custom_fn, tile_shape=(1, 512, 512))

Convert to OME-ZARR & view in napari

Optional plugins close the loop: convert any image (Imaris .ims, CZI, LIF, ND2, OME-TIFF, … via bioio) to a pyramidal, calibrated OME-ZARR, then view the image and its labels in napari.

from patchworks.plugins.ome_zarr import to_ome_zarr
from patchworks.plugins.napari import view_in_napari

to_ome_zarr("scan.ims", "scan.zarr")          # lazy, OOM-safe, keeps µm calibration
view_in_napari("scan.zarr", labels="scan.zarr/labels/labels")

Pyramids downsample X/Y only (Z kept full-res) and are built level-by-level from disk, so terabyte volumes convert in bounded RAM. See the OME-ZARR & napari guide.

From the command line

patchworks convert scan.czi scan.zarr
patchworks segment scan.zarr --method cellpose --model cyto3 --diameter 30 --gpu
patchworks info scan.zarr
patchworks view scan.zarr

See Command line for every method and flag.

Common patterns

Auto-size tiles from available memory

from patchworks import tile_process

tile_process("image.zarr", fn, tile_shape="auto", use_gpu=True)

Skip empty tiles (sparse volumes)

from patchworks import estimate_empty_tiles, tile_process

info = estimate_empty_tiles("image.zarr", tile_shape=(120, 697, 697))
print(f"{info['empty_fraction']:.0%} tiles are background — will be skipped")

tile_process(
    "image.zarr",
    fn,
    tile_shape=(120, 697, 697),
    skip_empty=True,
    empty_threshold=info["threshold"],
    write_to="labels.zarr",
)

Distributed cluster for GPU

from patchworks import make_local_cluster, tile_process

client, cluster = make_local_cluster(use_gpu=True)
try:
    tile_process("image.zarr", fn, write_to="labels.zarr", progress=True)
finally:
    client.close()
    cluster.close()

Contiguous label numbering

# Labels are globally unique by default, but may be gappy (block-encoded IDs).
# sequential_labels=True does a linear relabel O(voxels) — not O(n_tiles²).
tile_process("image.zarr", fn, write_to="labels.zarr", sequential_labels=True)

Use only the merge step (bring your own tiling)

If you already have per-tile labels from your own pipeline, just call the merge step directly:

import dask.array as da
import numpy as np
from patchworks import merge_tile_labels

# Your own tiling + segmentation
image = da.from_zarr("image.zarr").rechunk((1, 1024, 1024))
labeled = image.map_blocks(
    my_segment_fn, dtype="int32", meta=np.empty((0,) * image.ndim, dtype="int32")
)

merged = merge_tile_labels(labeled, write_to="labels.zarr", progress=True)

Or merge from a zarr store your pipeline already wrote:

from patchworks import merge_tile_labels

merged = merge_tile_labels(
    "my_staged_labels.zarr",
    input_component="raw_labels",
    write_to="merged.zarr",
    sequential_labels=True,
)

How tiling and merging work

See the Merging labels guide for a full explanation. Short version:

1. Image is split into tiles (with optional overlap for boundary context).
2. Your function is called independently on each tile. Dask handles parallelism and streaming — tiles are never all in memory at once.
3. Each tile's labels are written to a temp zarr exactly once (the staging step — this prevents your function being called 3-4× per tile during merge).
4. Thin slabs at each tile boundary are scanned for touching label pairs.
5. scipy connected components on the pairs → relabeling lookup table.
6. LUT applied to every tile in parallel → globally consistent labels.

The merge is zarr-native (no dask task graph), so it scales to thousands of tiles where the dask-image approach stalls.

Known pitfalls (and how patchworks avoids them)

Documentation

Full docs, guides and tutorials: https://imcf.one/patchworks/

• Getting Started
• User Guide — tiling, merging, empty-tile skipping, GPU/distributed, OME-ZARR & napari, pitfalls
• Examples — Cellpose, StarDist, custom functions, standalone merge
• API Reference · pdoc API

Requirements

• Python ≥ 3.11
• dask[array], numpy, zarr ≥ 3.1.3, scipy, psutil (RAM-aware tile and worker sizing)

Optional:

• nvidia-ml-py — accurate GPU VRAM sizing
• tqdm — progress bars
• cellpose — Cellpose plugin, v3 or v4 (patchworks[cellpose]); pin with [cellpose3] or [cellpose4]
• pycudadecon — deconvolution step of the dog plugin (patchworks[dog])
• bioio + readers — convert CZI/LIF/ND2/OME-TIFF/… to OME-ZARR (patchworks[bioio])
• imaris-ims-file-reader — convert Imaris .ims (patchworks[imaris])
• napari — interactive viewer plugin (patchworks[napari])
• cupy — install manually, matching your CUDA version (e.g. pip install cupy-cuda12x); not offered as an extra since it isn't one generic pin. Needed for use_gpu=True/dilate_gpu: true.

License

GNU General Public License v3.0 (GPL-3.0). See LICENSE.