Single-cell image mosaic

This example delegates h5sc tile preparation, edge filtering, and Apple-GPU photomosaic matching to scportrait.art.create_h5sc_collage. Make sure to install the required optional dependencies via pip install scportrait[art]

from pathlib import Path
import numpy as np
import scportrait
from scportrait.art import create_h5sc_collage

/Users/niklas/mamba/envs/260831_scp_art/lib/python3.11/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html
  from .autonotebook import tqdm as notebook_tqdm

datasets = scportrait.data.autophagosome_h5sc()

h5sc_path = Path(datasets[1])
master_png = Path("../../_static/scPortrait_logo_text.png")
output_png = Path("scPortrait_mosaic.png")

# RGB triplets
colors = np.array(
    [
        [215, 25, 32],
        [255, 209, 5],
        [59, 77, 129],
        # Add black for background
        [0, 0, 0],
    ],
    dtype=np.float32,
)

result = create_h5sc_collage(
    master_png=master_png,
    h5sc_path=h5sc_path,
    colors=colors,
    grid_width=50,
    n_samples_per_color=7,
    crop_size=128,
    channel_indices=slice(2, 6),
    edge_fraction_threshold=0.20,
    random_seed=492755,
    max_cell_uses=9,  # Maximum uses of each colorized channel/cell tile
    master_batch_size=128,
    tile_batch_size=10_000,
    output_path=output_png,
)

result.show()

Building mosaic: 100%|██████████| 500/500 [00:00<00:00, 25805.07it/s]