aind-hcr-data-loader 0.6.0

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aind-hcr-data-loader

Change log

v0.6.0 (03/18/2026)

New modules

• Added pairwise_dataset.py — create_pairwise_unmixing_dataset() for loading pairwise-unmixing pipeline outputs
• Added cell_typing_dataset.py — for attaching and querying cell-typing assets
• Added spot_filters.py — spot-level filtering by channel-intensity percentiles, spatial isolation (kdtree), and spectral purity

hcr_dataset.py

• Added create_hcr_dataset_from_schema() to construct an HCRDataset directly from an ophys-mfish-dataset-catalog JSON record (mice/<mouse_id>.json)
• create_hcr_dataset_from_config() now auto-attaches cell-typing assets when a "cell_typing" key is present in the mouse config and accepts a new metrics_base_path parameter
• HCRRound gains a parent_dataset reference (set automatically by create_hcr_dataset) enabling advanced filtering from round-level calls
• HCRRound.load_spots() gains an roi_filter_type parameter ('volume' or 'comprehensive') as a cleaner alternative to passing raw filter_cell_ids
• HCRDataset gains new methods: get_filtered_cell_ids(), create_cell_gene_matrix_from_spots(), load_taxonomy_cell_types(), load_taxonomy_cell_types_h5ad(), and annotate_with_cell_types()
• SpotFiles replaces the processing_manifest field with unmixed_cxg_filtered and mixed_cxg_filtered for pairwise-unmixing filtered CxG tables
• get_spot_files() now resolves pkl files using the round number from the key (e.g. R2 → mixed_spots_R2*.pkl) to avoid accidentally picking up artefact files (e.g. R-1)
• get_processing_manifests() now checks both derived/processing_manifest.json and the round root; raises FileNotFoundError with a clear message instead of an AssertionError
• create_channel_gene_table_from_manifests() now adds a round_channel_gene convenience column (e.g. "R2-488-GFP")
• create_channel_gene_table() parameter renamed from spot_files → processing_manifests to reflect that it now takes manifest dicts directly

filters.py

• roi_filter_soma_and_overlap() renamed to roi_filter_comprehensive() with an updated signature that no longer requires HCRDataset as a positional arg
• filter_tile_boundary_rois() signature updated for consistency
• Added filter_cell_info() — volume-quantile filter (default q1=0.2, q2=0.95) on a cell-info DataFrame
• Added get_inhibitory_mask() — returns a boolean mask for inhibitory cells based on per-gene thresholds

Dependencies

• Added pyarrow as a core dependency

v0.5.1 02/23/2026

• Added metrics_base_path parameter to HCRDataset for soma shape classifier
• Added new spot_filters.py module with vectorized percentile filtering and spot quality assessment functions
• Enhanced filters.py with comprehensive ROI filtering pipeline including soma classification, edge detection, and tile overlap filtering
• hcr_filters.ipynb notebook for filtering examples

v0.4.0 (10/16/2025)

• extract tile overlap boundaries
• adds ROI overlap calculation and filtering plus duplicate bbox plotting function.
• added linear unmixing to single cell plots
• new dye line plots
• new pairwise intensity plots
• added constants.py for channel colormaps
• gather neuroglancer links
• flexible figure saving via a new saveable_plot decorator

v0.3.8 (8/11/2025)

• updated how cell info is gathered from segmentation sources (options for r1 centroids.npy file or union of multi-round mixed/unmixed cell_x_gene tables).
• metrics path to segmentation files
• better error handling when missing spot files

Installation

To use the software, in the root directory, run

pip install -e .

To develop the code, run

pip install -e .[dev]

Contributing

Linters and testing

There are several libraries used to run linters, check documentation, and run tests.

• Please test your changes using the coverage library, which will run the tests and log a coverage report:

coverage run -m unittest discover && coverage report

• Use interrogate to check that modules, methods, etc. have been documented thoroughly:

interrogate .

• Use flake8 to check that code is up to standards (no unused imports, etc.):

flake8 .

• Use black to automatically format the code into PEP standards:

black .

• Use isort to automatically sort import statements:

isort .

Pull requests

For internal members, please create a branch. For external members, please fork the repository and open a pull request from the fork. We'll primarily use Angular style for commit messages. Roughly, they should follow the pattern:

<type>(<scope>): <short summary>

where scope (optional) describes the packages affected by the code changes and type (mandatory) is one of:

• build: Changes that affect build tools or external dependencies (example scopes: pyproject.toml, setup.py)
• ci: Changes to our CI configuration files and scripts (examples: .github/workflows/ci.yml)
• docs: Documentation only changes
• feat: A new feature
• fix: A bugfix
• perf: A code change that improves performance
• refactor: A code change that neither fixes a bug nor adds a feature
• test: Adding missing tests or correcting existing tests

Semantic Release

The table below, from semantic release, shows which commit message gets you which release type when semantic-release runs (using the default configuration):

Commit message	Release type
fix(pencil): stop graphite breaking when too much pressure applied	Patch Fix Release, Default release
feat(pencil): add 'graphiteWidth' option	Minor Feature Release
perf(pencil): remove graphiteWidth option BREAKING CHANGE: The graphiteWidth option has been removed. The default graphite width of 10mm is always used for performance reasons.	Major Breaking Release (Note that the BREAKING CHANGE: token must be in the footer of the commit)

Documentation

To generate the rst files source files for documentation, run

sphinx-apidoc -o docs/source/ src

Then to create the documentation HTML files, run

sphinx-build -b html docs/source/ docs/build/html

More info on sphinx installation can be found here.

Read the Docs Deployment

Note: Private repositories require Read the Docs for Business account. The following instructions are for a public repo.

The following are required to import and build documentations on Read the Docs:

• A Read the Docs user account connected to Github. See here for more details.
• Read the Docs needs elevated permissions to perform certain operations that ensure that the workflow is as smooth as possible, like installing webhooks. If you are not the owner of the repo, you may have to request elevated permissions from the owner/admin.
• A .readthedocs.yaml file in the root directory of the repo. Here is a basic template:

# Read the Docs configuration file
# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details

# Required
version: 2

# Set the OS, Python version, and other tools you might need
build:
  os: ubuntu-24.04
  tools:
    python: "3.13"

# Path to a Sphinx configuration file.
sphinx:
  configuration: docs/source/conf.py

# Declare the Python requirements required to build your documentation
python:
  install:
    - method: pip
      path: .
      extra_requirements:
        - dev

Here are the steps for building docs in Read the Docs. See here for detailed instructions:

• From Read the Docs dashboard, click on Add project.
• For automatic configuration, select Configure automatically and type the name of the repo. A repo with public visibility should appear as you type.
• Follow the subsequent steps.
• For manual configuration, select Configure manually and follow the subsequent steps

Once a project is created successfully, you will be able to configure/modify the project's settings; such as Default version, Default branch etc.