nViz Quickstart Guide#
This notebook helps demonstrate how to use nViz quickly.
We use demonstrational data found within this repository
to help show how the software works.
import pathlib
import shutil
from napari.utils import nbscreenshot
import nviz
# setup paths and prepare filesystem
test_image_dir = "../../../tests/data/random_tiff_z_stacks/Z99/"
test_label_dir = "../../../tests/data/random_tiff_z_stacks/labels/"
output_ome_tiff_path = "./example.ome.tiff"
output_zarr_path = "./example.zarr"
# scaling values in micrometers for z, y, and x dimensions.
# Note: This is typically a priori knowledge that is usually
# found in raw microscopy data (for example raw TIFF files
# or other microscopy metadata files [like XML]).
scaling_values = (1.0, 0.1, 0.1)
# If we already have a demo tiff file, remove it.
# (We are demoing the full nViz process from scratch.)
if (tiff_path := pathlib.Path(output_ome_tiff_path)).is_file():
tiff_path.unlink()
# If we already have a demo zarr dir, remove it
# (We are demoing the full nViz process from scratch.)
if (zarr_path := pathlib.Path(output_zarr_path)).is_dir():
shutil.rmtree(output_zarr_path)
# show our images
list(pathlib.Path(test_image_dir).rglob("*.tif"))
[PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_111_ZS025.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_555_ZS039.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_555_ZS004.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_111_ZS007.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_111_ZS011.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_444_ZS033.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_222_ZS043.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_333_ZS026.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_111_ZS016.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_444_ZS044.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_111_ZS027.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_222_ZS034.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_111_ZS019.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_222_ZS014.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_222_ZS001.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_444_ZS001.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_555_ZS029.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_555_ZS023.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_222_ZS022.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_555_ZS032.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_222_ZS030.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_222_ZS006.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_333_ZS036.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_333_ZS046.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_222_ZS046.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_222_ZS020.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_222_ZS037.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_555_ZS022.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_444_ZS046.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_555_ZS017.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_333_ZS024.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_111_ZS008.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_111_ZS026.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_444_ZS026.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_222_ZS026.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_444_ZS009.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_444_ZS037.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_111_ZS045.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_333_ZS008.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_555_ZS033.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_222_ZS011.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_111_ZS002.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_333_ZS045.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_333_ZS039.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_222_ZS040.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_555_ZS009.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_444_ZS022.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_555_ZS028.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_111_ZS034.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_444_ZS020.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_111_ZS042.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_555_ZS021.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_555_ZS003.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_555_ZS011.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_444_ZS035.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_222_ZS018.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_111_ZS017.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_222_ZS032.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_333_ZS047.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_555_ZS044.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_333_ZS035.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_444_ZS004.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_222_ZS013.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_444_ZS028.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_222_ZS012.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_444_ZS041.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_333_ZS017.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_222_ZS035.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_555_ZS034.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_333_ZS000.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_111_ZS037.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_111_ZS023.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_444_ZS005.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_444_ZS017.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_111_ZS035.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_555_ZS026.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_333_ZS031.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_111_ZS005.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_333_ZS004.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_444_ZS040.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_222_ZS015.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_444_ZS025.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_222_ZS005.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_333_ZS010.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_111_ZS003.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_444_ZS002.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_222_ZS045.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_555_ZS040.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_222_ZS042.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_444_ZS042.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_444_ZS047.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_111_ZS012.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_333_ZS020.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_555_ZS000.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_333_ZS013.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_555_ZS045.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_111_ZS032.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_444_ZS000.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_333_ZS018.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_444_ZS014.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_444_ZS036.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_333_ZS033.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_444_ZS039.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_333_ZS042.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_444_ZS006.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_333_ZS007.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_555_ZS038.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_555_ZS042.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_333_ZS006.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_333_ZS003.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_555_ZS037.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_222_ZS041.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_555_ZS014.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_555_ZS005.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_222_ZS016.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_111_ZS033.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_333_ZS030.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_333_ZS011.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_444_ZS008.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_222_ZS021.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_444_ZS023.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_333_ZS038.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_111_ZS036.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_444_ZS024.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_222_ZS008.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_333_ZS040.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_111_ZS046.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_444_ZS029.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_111_ZS040.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_333_ZS032.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_222_ZS017.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_555_ZS010.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_222_ZS019.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_222_ZS004.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_444_ZS013.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_555_ZS030.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_555_ZS015.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_222_ZS023.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_222_ZS036.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_222_ZS000.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_444_ZS007.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_111_ZS014.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_555_ZS025.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_444_ZS030.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_222_ZS031.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_333_ZS005.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_555_ZS047.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_111_ZS043.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_333_ZS016.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_444_ZS032.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_333_ZS002.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_111_ZS020.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_222_ZS002.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_555_ZS016.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_111_ZS021.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_111_ZS001.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_444_ZS034.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_222_ZS028.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_333_ZS025.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_222_ZS010.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_555_ZS006.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_555_ZS024.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_555_ZS019.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_333_ZS037.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_555_ZS035.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_111_ZS022.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_111_ZS038.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_555_ZS002.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_333_ZS014.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_111_ZS039.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_222_ZS029.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_555_ZS020.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_555_ZS031.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_333_ZS021.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_333_ZS001.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_111_ZS041.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_333_ZS019.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_111_ZS018.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_555_ZS007.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_333_ZS009.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_555_ZS036.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_111_ZS013.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_111_ZS028.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_444_ZS018.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_333_ZS015.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_333_ZS022.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_111_ZS004.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_222_ZS009.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_333_ZS012.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_222_ZS044.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_111_ZS009.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_222_ZS027.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_333_ZS029.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_444_ZS003.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_222_ZS038.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_444_ZS045.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_555_ZS043.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_444_ZS019.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_555_ZS012.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_222_ZS033.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_444_ZS031.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_111_ZS044.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_111_ZS024.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_111_ZS030.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_555_ZS041.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_555_ZS027.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_444_ZS021.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_444_ZS012.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_555_ZS018.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_222_ZS039.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_111_ZS047.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_333_ZS043.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_555_ZS008.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_444_ZS011.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_444_ZS010.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_222_ZS024.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_111_ZS015.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_444_ZS016.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_333_ZS028.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_333_ZS041.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_111_ZS031.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_222_ZS007.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_111_ZS000.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_111_ZS006.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_333_ZS027.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_111_ZS029.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_222_ZS047.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_555_ZS013.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_444_ZS027.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_555_ZS001.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_222_ZS003.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_333_ZS044.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_222_ZS025.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_333_ZS034.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_555_ZS046.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_333_ZS023.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_444_ZS043.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_444_ZS015.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_111_ZS010.tif'),
PosixPath('../../../tests/data/random_tiff_z_stacks/Z99/Z99_444_ZS038.tif')]
# show our label files (in this case, segmentation masks)
# Other labels might include outlines, bounding boxes,
# or similar data stored as images which provide
# information about objects of interest.
list(pathlib.Path(test_label_dir).rglob("*.tif"))
[PosixPath('../../../tests/data/random_tiff_z_stacks/labels/compartment.tif')]
# convert original raw TIFF into OME-TIFF format using nViz
nviz_ome_tiff = nviz.tiff_to_ometiff(
# specify an image directory (original images)
image_dir=test_image_dir,
# specify a label (masks or outlines) directory
label_dir=test_label_dir,
# specify an output path
output_path=output_ome_tiff_path,
# Map filename patterns to channel names.
# Note: the keys of this dictionary correspond to information
# found in the file name. The value pairs are customizable, and
# they will display as specified here inside a Napari window.
channel_map={
"111": "Channel A",
"222": "Channel B",
"333": "Channel C",
"444": "Channel D",
"555": "Channel E",
},
# set the scaling for z, y, and x
scaling_values=scaling_values,
)
# show the filepath
nviz_ome_tiff
'./example.ome.tiff'
# view the ome-tiff in napari
# (will open a new window and also returns the viewer object)
viewer = nviz.view_ometiff_with_napari(
ometiff_path=nviz_ome_tiff, scaling_values=scaling_values, headless=True
)
Running view in headless mode and returning a napari viewer object.
# show the napari window within this notebook to help demonstrate output
viewer.window.resize(1300, 1100)
viewer.camera.angles = (70, 30, 40)
viewer.camera.zoom = 15
nbscreenshot(viewer=viewer, canvas_only=False)
# convert original data into a Zarr which
# includes OME-Zarr images format using nViz
nviz_zarr = nviz.tiff_to_zarr(
# specify an image directory (original images)
image_dir=test_image_dir,
# specify a label (masks or outlines) directory
label_dir=test_label_dir,
# specify an output path
output_path=output_zarr_path,
# Map filename patterns to channel names.
# Note: the keys of this dictionary correspond to information
# found in the file name. The value pairs are customizable, and
# they will display as specified here inside a Napari window.
channel_map={
"111": "Channel A",
"222": "Channel B",
"333": "Channel C",
"444": "Channel D",
"555": "Channel E",
},
# set the scaling for z, y, and x
scaling_values=scaling_values,
)
# show the filepath
nviz_zarr
'./example.zarr'
# view the zarr in napari
# (will open a new window and also returns the viewer object)
viewer = nviz.view_zarr_with_napari(
zarr_dir=output_zarr_path, scaling_values=scaling_values, headless=True
)
Running view in headless mode and returning a napari viewer object.
# show the napari window within this notebook to help demonstrate output
viewer.window.resize(1300, 1100)
viewer.camera.angles = (-30, 10, 40)
viewer.camera.zoom = 15
nbscreenshot(viewer=viewer, canvas_only=False)
