.gitignore
.pre-commit-config.yaml
LICENSE
MANIFEST.in
README.md
mkdocs.yml
pyproject.toml
tox.ini
uv.lock
.github/instructions/environments.instructions.md
.github/instructions/quickstart.instructions.md
.github/workflows/browser.yml
.github/workflows/documentation_main.yml
.github/workflows/documentation_release.yml
.github/workflows/test_and_deploy.yml
.github/workflows/test_cron.yml
docs/built_in_methods_fusion.md
docs/built_in_methods_global_param_resolution.md
docs/built_in_methods_pairwise_registration.md
docs/chart.md
docs/code_example.md
docs/contributing.md
docs/data_formats.md
docs/data_loading_overview.md
docs/docs_requirements.txt
docs/extension_api_fusion.md
docs/extension_api_global_param_resolution.md
docs/extension_api_pairwise_registration.md
docs/features.md
docs/fusion_overview.md
docs/gpu_support.md
docs/implementation_details.md
docs/index.md
docs/installation.md
docs/napari_stitcher.md
docs/neuroglancer.md
docs/objects.md
docs/registration_metrics.md
docs/registration_overview.md
docs/related_projects.md
docs/stitching_in_the_browser.md
docs/troubleshoot_fusion.md
docs/troubleshoot_multiprocessing.md
docs/troubleshoot_registration_OOM.md
docs/troubleshoot_registration_accuracy.md
docs/zarr_backed_vs_dask_backed_fusion.md
docs/api/fusion.md
docs/api/metrics.md
docs/api/registration.md
docs/browser/app.css
docs/browser/app.js
docs/browser/camera.js
docs/browser/compute-worker.js
docs/browser/config.json
docs/browser/fs-worker.js
docs/browser/highlight.js
docs/browser/index.html
docs/browser/jobs.js
docs/browser/logo.svg
docs/browser/placement.js
docs/browser/py-runtime.js
docs/browser/routes.js
docs/browser/session-worker.js
docs/browser/sw.js
docs/browser/viewer.js
docs/images/20230929_screenshot.png
docs/images/applications_mosaic.png
docs/images/example_vis_utils.png
docs/images/global_registration_summary_example.png
docs/images/logo.png
docs/images/logo.svg
docs/images/logo_blue.svg
docs/images/logo_color.png
docs/images/logo_color.svg
docs/images/metrics_tile_pair_cross_corr.png
docs/images/metrics_tile_pair_cross_corr_fine.png
docs/images/metrics_tile_pair_pairwise_plot.png
docs/images/neuroglancer_acind.jpg
docs/images/pairwise_registration_summary_example.png
docs/images/registration_summary_pairwise.png
docs/images/registration_summary_plot_groupwise.png
docs/images/tile_configuration.png
docs/images/workflow_schematic.png
notebooks/multiview_reconstruction.ipynb
notebooks/stitch_and_register_ashlar_example_dataset.ipynb
notebooks/stitching_bigstitcher_grid_2d_ome_zarr.ipynb
notebooks/stitching_bigstitcher_grid_3d_ome_zarr.ipynb
notebooks/stitching_bigstitcher_multiview.ipynb
notebooks/stitching_exaspim.ipynb
notebooks/stitching_in_the_browser.ipynb
notebooks/stitching_mesospim.ipynb
notebooks/stitching_multipos_2D_czi.ipynb
scripts/build_browser_app.py
src/multiview_stitcher/__init__.py
src/multiview_stitcher/_version.py
src/multiview_stitcher/_zarr_compat.py
src/multiview_stitcher/czi_utils.py
src/multiview_stitcher/czifile_patch.py
src/multiview_stitcher/detection.py
src/multiview_stitcher/elastix.py
src/multiview_stitcher/imaris_utils.py
src/multiview_stitcher/io.py
src/multiview_stitcher/metrics.py
src/multiview_stitcher/misc_utils.py
src/multiview_stitcher/msi_utils.py
src/multiview_stitcher/mv_graph.py
src/multiview_stitcher/neuroglancer.py
src/multiview_stitcher/ngff_utils.py
src/multiview_stitcher/param_utils.py
src/multiview_stitcher/registration.py
src/multiview_stitcher/sample_data.py
src/multiview_stitcher/spatial_image_utils.py
src/multiview_stitcher/tif_utils.py
src/multiview_stitcher/transformation.py
src/multiview_stitcher/transforms.py
src/multiview_stitcher/vis_utils.py
src/multiview_stitcher/weights.py
src/multiview_stitcher/zarr_utils.py
src/multiview_stitcher.egg-info/PKG-INFO
src/multiview_stitcher.egg-info/SOURCES.txt
src/multiview_stitcher.egg-info/dependency_links.txt
src/multiview_stitcher.egg-info/requires.txt
src/multiview_stitcher.egg-info/scm_file_list.json
src/multiview_stitcher.egg-info/scm_version.json
src/multiview_stitcher.egg-info/top_level.txt
src/multiview_stitcher/_benchmarks/__init__.py
src/multiview_stitcher/_benchmarks/test_core.py
src/multiview_stitcher/_tests/__init__.py
src/multiview_stitcher/_tests/_create_test_params.ipynb
src/multiview_stitcher/_tests/test_bayesian_fusion.py
src/multiview_stitcher/_tests/test_bench.py
src/multiview_stitcher/_tests/test_browser.py
src/multiview_stitcher/_tests/test_detection.py
src/multiview_stitcher/_tests/test_fusion.py
src/multiview_stitcher/_tests/test_integration.py
src/multiview_stitcher/_tests/test_io.py
src/multiview_stitcher/_tests/test_metrics.py
src/multiview_stitcher/_tests/test_msi_utils.py
src/multiview_stitcher/_tests/test_mv_graph.py
src/multiview_stitcher/_tests/test_ngff_utils.py
src/multiview_stitcher/_tests/test_param_resolution.py
src/multiview_stitcher/_tests/test_param_utils.py
src/multiview_stitcher/_tests/test_quickstart.py
src/multiview_stitcher/_tests/test_registration.py
src/multiview_stitcher/_tests/test_sample_data.py
src/multiview_stitcher/_tests/test_spatial_image_utils.py
src/multiview_stitcher/_tests/test_tif_utils.py
src/multiview_stitcher/_tests/test_transformation.py
src/multiview_stitcher/_tests/test_vis_utils.py
src/multiview_stitcher/_tests/test_weights.py
src/multiview_stitcher/_tests/test_zarr_utils.py
src/multiview_stitcher/_tests/quickstart/0_data_preparation.py
src/multiview_stitcher/_tests/quickstart/1_registration.py
src/multiview_stitcher/_tests/quickstart/2_fusion.py
src/multiview_stitcher/_tests/quickstart/3_fusion_large.py
src/multiview_stitcher/browser/AGENTS.md
src/multiview_stitcher/browser/CLAUDE.md
src/multiview_stitcher/browser/__init__.py
src/multiview_stitcher/browser/bridge.py
src/multiview_stitcher/browser/czi.py
src/multiview_stitcher/browser/dataset.py
src/multiview_stitcher/browser/elastix.py
src/multiview_stitcher/browser/env.py
src/multiview_stitcher/browser/example_data.py
src/multiview_stitcher/browser/executors.py
src/multiview_stitcher/browser/fusion.py
src/multiview_stitcher/browser/serialization.py
src/multiview_stitcher/browser/session.py
src/multiview_stitcher/browser/specs.py
src/multiview_stitcher/browser/store.py
src/multiview_stitcher/browser/worker.py
src/multiview_stitcher/fusion/__init__.py
src/multiview_stitcher/fusion/_core.py
src/multiview_stitcher/fusion/mv_deconv.py
src/multiview_stitcher/param_resolution/__init__.py
src/multiview_stitcher/param_resolution/global_optimization.py
src/multiview_stitcher/param_resolution/linear_two_pass.py
src/multiview_stitcher/param_resolution/shortest_paths.py
src/multiview_stitcher/param_resolution/utils.py
src/multiview_stitcher/test-datasets/mosaic_test.czi
tests/browser/boot_timing.mjs
tests/browser/camera.test.mjs
tests/browser/dump_route_fixtures.py
tests/browser/fixtures.json
tests/browser/highlight.test.mjs
tests/browser/jobs.test.mjs
tests/browser/package-lock.json
tests/browser/package.json
tests/browser/placement.test.mjs
tests/browser/pyodide_lock.test.mjs
tests/browser/routes.test.mjs
tests/browser/smoke.mjs
tests/browser/smoke.py