copick-utils 1.0.2__tar.gz → 1.2.0__tar.gz

{copick_utils-1.0.2 → copick_utils-1.2.0}/.github/workflows/conventional-commits.yml

@@ -16,4 +16,4 @@ jobs:
   conventional_commit_title:
     runs-on: ubuntu-latest
     steps:
-      - uses: chanzuckerberg/github-actions/.github/actions/conventional-commits@v6.12.2
+      - uses: chanzuckerberg/github-actions/.github/actions/conventional-commits@v6.13.0

copick_utils-1.2.0/.release-please.manifest.json

@@ -0,0 +1,3 @@
+{
+  ".": "1.2.0"
+}

{copick_utils-1.0.2 → copick_utils-1.2.0}/CHANGELOG.md

@@ -1,5 +1,29 @@
 # Changelog
 
+## [1.2.0](https://github.com/copick/copick-utils/compare/copick-utils-v1.1.0...copick-utils-v1.2.0) (2026-01-31)
+
+
+### ✨ Features
+
+* add parser uri to readers, add function to download portal project fo… ([#43](https://github.com/copick/copick-utils/issues/43)) ([7743ee5](https://github.com/copick/copick-utils/commit/7743ee5facb6dff037f8348852c6edcd105abe25))
+
+
+### 🐞 Bug Fixes
+
+* URI in copick readers ([#45](https://github.com/copick/copick-utils/issues/45)) ([926f01d](https://github.com/copick/copick-utils/commit/926f01dfccb537bca90fd30ee59ceacb83d7f947))
+
+## [1.1.0](https://github.com/copick/copick-utils/compare/copick-utils-v1.0.2...copick-utils-v1.1.0) (2026-01-26)
+
+
+### ✨ Features
+
+* Add split command. ([#41](https://github.com/copick/copick-utils/issues/41)) ([479bf48](https://github.com/copick/copick-utils/commit/479bf48f9a50e3eb4066b3a41f2b399f110b2553))
+
+
+### 🐞 Bug Fixes
+
+* bump chanzuckerberg/github-actions from 6.12.2 to 6.13.0 ([#40](https://github.com/copick/copick-utils/issues/40)) ([68b21c1](https://github.com/copick/copick-utils/commit/68b21c175e2ca96946ceba9252b86c17e3382fe2))
+
 ## [1.0.2](https://github.com/copick/copick-utils/compare/copick-utils-v1.0.1...copick-utils-v1.0.2) (2026-01-06)
 
 

{copick_utils-1.0.2 → copick_utils-1.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: copick-utils
-Version: 1.0.2
+Version: 1.2.0
 Summary: Utilities for copick
 Project-URL: Repository, https://github.com/KyleHarrington/copick-utils.git
 Project-URL: Issues, https://github.com/KyleHarrington/copick-utils/issues
@@ -33,6 +33,7 @@ Requires-Dist: click-option-group
 Requires-Dist: copick>=1.16.0
 Requires-Dist: manifold3d
 Requires-Dist: mapbox-earcut
+Requires-Dist: mdocfile
 Requires-Dist: numpy
 Requires-Dist: rtree
 Requires-Dist: scikit-image

{copick_utils-1.0.2 → copick_utils-1.2.0}/pyproject.toml

@@ -29,6 +29,7 @@ dependencies = [
     "trimesh",
     "manifold3d",
     "mapbox-earcut",
+    "mdocfile",
     "tqdm",
     "scikit-learn",
     "shapely",
@@ -76,6 +77,7 @@ skeletonize = "copick_utils.cli.processing_commands:skeletonize"
 fit_spline = "copick_utils.cli.processing_commands:fit_spline"
 validbox = "copick_utils.cli.processing_commands:validbox"
 hull = "copick_utils.cli.processing_commands:hull"
+split = "copick_utils.cli.processing_commands:split"
 
 [project.entry-points."copick.logical.commands"]
 meshop = "copick_utils.cli.logical_commands:meshop"
@@ -87,6 +89,9 @@ clippicks = "copick_utils.cli.logical_commands:clippicks"
 picksin = "copick_utils.cli.logical_commands:picksin"
 picksout = "copick_utils.cli.logical_commands:picksout"
 
+[project.entry-points."copick.download.commands"]
+project = "copick_utils.cli.download_commands:project"
+
 [tool.hatch.version]
 path = "src/copick_utils/__init__.py"
 

{copick_utils-1.0.2 → copick_utils-1.2.0}/src/copick_utils/__init__.py

@@ -1,4 +1,4 @@
 # SPDX-FileCopyrightText: 2024-present Kyle Harrington <czi@kyleharrington.com>
 #
 # SPDX-License-Identifier: MIT
-__version__ = "1.0.2"
+__version__ = "1.2.0"

copick_utils-1.2.0/src/copick_utils/cli/download.py

@@ -0,0 +1,34 @@
+import click
+
+
+@click.command(
+    context_settings={"show_default": True},
+    short_help="Download tilt series and alignments from the CryoET Data Portal.",
+    no_args_is_help=True,
+)
+@click.option(
+    "-ds",
+    "--dataset",
+    required=True,
+    type=str,
+    help="Dataset ID to download from the CryoET Data Portal.",
+)
+@click.option(
+    "-o",
+    "--output",
+    required=True,
+    default=".",
+    type=str,
+    help="Output directory to save the downloaded files.",
+)
+def project(dataset: str, output: str):
+    """
+    Download tilt series and alignments from the CryoET Data Portal for sub-tomogram averaging with py2rely.
+    """
+    download_project(dataset, output)
+
+
+def download_project(dataset: str, output: str):
+    import copick_utils.io.portal as portal
+
+    portal.download_aretomo_files(dataset, output)

copick_utils-1.2.0/src/copick_utils/cli/download_commands.py

@@ -0,0 +1,11 @@
+"""CLI commands for downloading data from the CryoET Data Portal.
+
+This module imports all download commands from specialized files for better organization.
+"""
+
+from copick_utils.cli.download import project
+
+# All commands are now available for import by the main CLI
+__all__ = [
+    "project",
+]

{copick_utils-1.0.2 → copick_utils-1.2.0}/src/copick_utils/cli/processing_commands.py

@@ -5,6 +5,7 @@ from copick_utils.cli.fit_spline import fit_spline
 from copick_utils.cli.hull import hull
 from copick_utils.cli.separate_components import separate_components
 from copick_utils.cli.skeletonize import skeletonize
+from copick_utils.cli.split_labels import split
 from copick_utils.cli.validbox import validbox
 
 # All commands are now available for import by the main CLI
@@ -15,4 +16,5 @@ __all__ = [
     "separate_components",
     "filter_components",
     "fit_spline",
+    "split",
 ]

copick_utils-1.2.0/src/copick_utils/cli/split_labels.py

@@ -0,0 +1,148 @@
+"""CLI command for splitting multilabel segmentations into individual single-class segmentations."""
+
+import click
+import copick
+from click_option_group import optgroup
+from copick.cli.util import add_config_option, add_debug_option
+from copick.util.log import get_logger
+from copick.util.uri import parse_copick_uri
+
+from copick_utils.cli.util import add_input_option, add_workers_option
+
+
+@click.command(
+    context_settings={"show_default": True},
+    short_help="Split multilabel segmentations into single-class segmentations.",
+    no_args_is_help=True,
+)
+@add_config_option
+@optgroup.group("\nInput Options", help="Options related to the input segmentation.")
+@optgroup.option(
+    "--run-names",
+    "-r",
+    multiple=True,
+    help="Specific run names to process (default: all runs).",
+)
+@add_input_option("segmentation")
+@optgroup.group("\nTool Options", help="Options related to this tool.")
+@add_workers_option
+@optgroup.group("\nOutput Options", help="Options related to output segmentations.")
+@optgroup.option(
+    "--output-user-id",
+    type=str,
+    default="split",
+    help="User ID for output segmentations.",
+)
+@add_debug_option
+def split(
+    config,
+    run_names,
+    input_uri,
+    workers,
+    output_user_id,
+    debug,
+):
+    """
+    Split multilabel segmentations into individual single-class binary segmentations.
+
+    This command takes a multilabel segmentation and creates separate binary segmentations
+    for each label value. Each output segmentation is named after the corresponding
+    PickableObject (as defined in the copick config) and uses the same session ID as
+    the input.
+
+    \b
+    URI Format:
+        Segmentations: name:user_id/session_id@voxel_spacing
+
+    \b
+    Label-to-Object Mapping:
+        The tool looks up each label value in the pickable_objects configuration
+        and uses the object name for the output segmentation:
+        - Label 1 (ribosome) → ribosome:split/session-001@10.0
+        - Label 2 (membrane) → membrane:split/session-001@10.0
+        - Label 3 (proteasome) → proteasome:split/session-001@10.0
+
+    \b
+    Examples:
+        # Split multilabel segmentation (outputs named by pickable objects)
+        copick process split -i "predictions:model/run-001@10.0"
+
+        # Split with custom output user ID
+        copick process split -i "classes:annotator/manual@10.0" --output-user-id "per-class"
+
+        # Process specific runs only
+        copick process split -i "labels:*/*@10.0" --run-names TS_001 --run-names TS_002
+    """
+
+    logger = get_logger(__name__, debug=debug)
+
+    root = copick.from_file(config)
+    run_names_list = list(run_names) if run_names else None
+
+    # Parse input URI
+    try:
+        input_params = parse_copick_uri(input_uri, "segmentation")
+    except ValueError as e:
+        raise click.BadParameter(f"Invalid input URI: {e}") from e
+
+    segmentation_name = input_params["name"]
+    segmentation_user_id = input_params["user_id"]
+    segmentation_session_id = input_params["session_id"]
+    voxel_spacing = input_params.get("voxel_spacing")
+
+    if voxel_spacing is None or voxel_spacing == "*":
+        raise click.BadParameter("Input URI must include a specific voxel spacing (e.g., @10.0)")
+
+    # Check for patterns in critical fields
+    if "*" in segmentation_name or "*" in segmentation_user_id or "*" in segmentation_session_id:
+        raise click.BadParameter(
+            "Input URI cannot contain wildcards for splitting. "
+            "Please specify exact segmentation name, user_id, and session_id.",
+        )
+
+    logger.info(f"Splitting multilabel segmentation '{segmentation_name}'")
+    logger.debug(f"Input: {segmentation_user_id}/{segmentation_session_id} @ {voxel_spacing}Å")
+    logger.debug(f"Output user ID: {output_user_id}")
+    logger.debug(f"Workers: {workers}")
+
+    # Import batch function
+    from copick_utils.process.split_labels import split_labels_batch
+
+    # Process runs
+    results = split_labels_batch(
+        root=root,
+        segmentation_name=segmentation_name,
+        segmentation_user_id=segmentation_user_id,
+        segmentation_session_id=segmentation_session_id,
+        voxel_spacing=float(voxel_spacing),
+        output_user_id=output_user_id,
+        run_names=run_names_list,
+        workers=workers,
+    )
+
+    # Aggregate results
+    successful = sum(1 for result in results.values() if result and result.get("processed", 0) > 0)
+    total_labels = sum(result.get("labels_split", 0) for result in results.values() if result)
+
+    # Collect all unique object names created
+    all_object_names = set()
+    for result in results.values():
+        if result and result.get("object_names"):
+            all_object_names.update(result["object_names"])
+
+    # Collect all errors
+    all_errors = []
+    for result in results.values():
+        if result and result.get("errors"):
+            all_errors.extend(result["errors"])
+
+    logger.info(f"Completed: {successful}/{len(results)} runs processed successfully")
+    logger.info(f"Total labels split: {total_labels}")
+    logger.info(f"Object names created: {', '.join(sorted(all_object_names))}")
+
+    if all_errors:
+        logger.warning(f"Encountered {len(all_errors)} errors during processing")
+        for error in all_errors[:5]:  # Show first 5 errors
+            logger.warning(f"  - {error}")
+        if len(all_errors) > 5:
+            logger.warning(f"  ... and {len(all_errors) - 5} more errors")

copick_utils-1.2.0/src/copick_utils/io/portal.py

@@ -0,0 +1,149 @@
+"""
+A minimal example using minimal libraries / imports to download relevant AreTomo files
+from the CryoET Data Portal. Downloads the corresponding files, using the run ID as the
+base filename.
+
+Original implementation by Daniel Ji and Utz Ermel.
+"""
+import multiprocessing
+import os
+
+import cryoet_data_portal as cdp
+import mdocfile
+import numpy as np
+import pandas as pd
+import requests
+import s3fs
+
+global_client = cdp.Client()
+
+
+def download_aretomo_files(dataset_id: int, output_dir: str):
+    print(f"Fetching tiltseries for dataset id {dataset_id}...", flush=True)
+    tiltseries_list: list[cdp.TiltSeries] = [
+        tiltseries for run in cdp.Dataset.get_by_id(global_client, dataset_id).runs for tiltseries in run.tiltseries
+    ]  # a bit slow for some reason, can take some time
+    tiltseries_run_ids_and_ts_ids = [(ts.run.id, ts.id) for ts in tiltseries_list]
+    print(
+        f"Found {len(tiltseries_run_ids_and_ts_ids)} tiltseries for dataset id {dataset_id}. Starting downloads...",
+        flush=True,
+    )
+    with multiprocessing.Pool(processes=8) as pool:  # adjust number of processes as needed
+        for _ in pool.imap_unordered(
+            _worker_download_aretomo_files_for_tiltseries,
+            [
+                (dataset_id, run_name, output_dir, tiltseries_id)
+                for run_name, tiltseries_id in tiltseries_run_ids_and_ts_ids
+            ],
+        ):
+            pass
+
+
+def _worker_download_aretomo_files_for_tiltseries(args):
+    dataset_id, run_name, output_dir, tiltseries_id = args
+    download_aretomo_files_for_tiltseries(dataset_id, run_name, output_dir, tiltseries_id)
+
+
+# note: this function assumes that there is only one tiltseries per run
+# note: the tiltseries name is equivlaent to the run name
+# if tiltseries_id is provided, will be prioritized over dataset_id + run_name
+def download_aretomo_files_for_tiltseries(dataset_id: int, run_name: str, output_dir: str, tiltseries_id: int = None):
+    print(f"[{run_name}] Downloading AreTomo files for tiltseries id {tiltseries_id}...", flush=True)
+
+    client = cdp.Client()
+    s3 = s3fs.S3FileSystem(anon=True)
+    if not tiltseries_id:
+        all_tiltseries = cdp.TiltSeries.find(
+            client,
+            query_filters=[cdp.TiltSeries.run.dataset_id == dataset_id, cdp.TiltSeries.run.name == run_name],
+        )
+        if len(all_tiltseries) == 0:
+            raise ValueError(f"No tiltseries found for dataset_id {dataset_id} and run_name {run_name}")
+        if len(all_tiltseries) > 1:
+            raise ValueError(f"Multiple tiltseries found for dataset_id {dataset_id} and run_name {run_name}")
+        tiltseries = all_tiltseries[0]
+    else:
+        tiltseries = cdp.TiltSeries.get_by_id(client, tiltseries_id)
+
+    # get the s3 folder path and then glob for *.tlt / *.rawtlt files to download them, renaming the base to match the run id
+    s3_folder_path = tiltseries.s3_mrc_file.rsplit("/", 1)[0] + "/"
+    tlt_files = s3.glob(s3_folder_path + "*.tlt") + s3.glob(s3_folder_path + "*.rawtlt")
+    for tlt_file in tlt_files:
+        base_name = os.path.basename(tlt_file)
+        ext = os.path.splitext(base_name)[1]
+        dest_file = os.path.join(output_dir, f"{tiltseries.run.id}{ext}")
+        s3.get(tlt_file, dest_file)
+        print(f"[{tiltseries.run.id}] Downloaded {base_name} as {os.path.basename(dest_file)}.", flush=True)
+
+    # do the same for "*CTF*.txt" files and "*ctf*.txt" files
+    ctf_files = s3.glob(s3_folder_path + "*CTF*.txt") + s3.glob(s3_folder_path + "*ctf*.txt")
+    if len(ctf_files) == 0:
+        print(f"WARNING: No CTF files found for tiltseries id {tiltseries.id}")
+    else:
+        ctf_file = ctf_files[0]
+        base_name = os.path.basename(ctf_file)
+        if len(ctf_files) > 1:
+            print(f"WARNING: Multiple CTF files found for tiltseries id {tiltseries.id}, using {base_name}")
+        ext = os.path.splitext(base_name)[1]
+        dest_file = os.path.join(output_dir, f"{tiltseries.run.id}_CTF.txt")
+        s3.get(ctf_file, dest_file)
+        print(f"[{tiltseries.run.id}] Downloaded {base_name} as {os.path.basename(dest_file)}.", flush=True)
+
+    # now find the corresponding alignment for this tiltseries and download the "*.aln" file
+    if len(tiltseries.alignments) == 0:
+        print(f"WARNING: No alignments found for tiltseries id {tiltseries.id}")
+    elif len(tiltseries.alignments) > 1:
+        print(f"WARNING: Multiple alignments found for tiltseries id {tiltseries.id}")
+    else:
+        alignment = tiltseries.alignments[0]
+        s3_alignment_folder_path = alignment.s3_alignment_metadata.rsplit("/", 1)[0] + "/"
+        aln_files = s3.glob(s3_alignment_folder_path + "*.aln")
+        if len(aln_files) == 0:
+            raise ValueError(f"No .aln files found for run name {tiltseries.run.name} and alignment id {alignment.id}")
+        aln_file = aln_files[0]
+        base_name = os.path.basename(aln_file)
+        if len(aln_files) > 1:
+            print(f"WARNING: Multiple .aln files found for run name {tiltseries.run.name}, using {base_name}")
+        ext = os.path.splitext(base_name)[1]
+        dest_file = os.path.join(output_dir, f"{tiltseries.run.id}{ext}")
+        s3.get(aln_file, dest_file)
+        print(f"[{tiltseries.run.id}] Downloaded {base_name} as {os.path.basename(dest_file)}.", flush=True)
+
+    # now get the mdoc file from the Frames/ folder
+    frames = tiltseries.run.frames
+    if len(frames) == 0:
+        raise ValueError(f"No frames found for run name {tiltseries.run.name}")
+    frame = frames[0]
+    s3_frames_folder_path = frame.s3_frame_path.rsplit("/", 1)[0] + "/"
+    mdoc_files = s3.glob(s3_frames_folder_path + "*.mdoc")
+    if len(mdoc_files) == 0:
+        raise ValueError(f"No .mdoc files found for run name {tiltseries.run.name}")
+    mdoc_file = mdoc_files[0]
+    base_name = os.path.basename(mdoc_file)
+    if len(mdoc_files) > 1:
+        print(f"WARNING: Multiple .mdoc files found for run name {tiltseries.run.name}, using {base_name}")
+    ext = os.path.splitext(base_name)[1]
+    dest_file = os.path.join(output_dir, f"{tiltseries.run.id}{ext}")
+    s3.get(mdoc_file, dest_file)
+    print(f"[{tiltseries.run.id}] Downloaded {base_name} as {os.path.basename(dest_file)}.", flush=True)
+
+    # download tiltseries mrc file
+    tiltseries_file = os.path.join(output_dir, f"{tiltseries.run.id}.mrc")
+    tiltseries_url = tiltseries.https_mrc_file
+    response = requests.get(tiltseries_url, stream=True)
+    response.raise_for_status()
+    with open(tiltseries_file, "wb") as f:
+        for chunk in response.iter_content(chunk_size=8192):
+            f.write(chunk)
+    print(f"[{tiltseries.run.id}] Downloaded tiltseries mrc file as {os.path.basename(tiltseries_file)}.", flush=True)
+
+    # create imod file for order list
+    mdoc = mdocfile.read(os.path.join(output_dir, f"{tiltseries.run.id}.mdoc"))
+    order_list = mdoc["TiltAngle"]
+    imodpath = os.path.join(output_dir, f"{tiltseries.run.id}_Imod")
+    os.makedirs(imodpath, exist_ok=True)
+    number = np.arange(len(order_list)) + 1
+
+    # save in csv with 'ImageNumber', 'TiltAngle' headers
+    df = pd.DataFrame({"ImageNumber": number, "TiltAngle": order_list})
+    df.to_csv(os.path.join(imodpath, f"{tiltseries.run.id}_order_list.csv"), index=False)

copick_utils-1.2.0/src/copick_utils/io/readers.py

@@ -0,0 +1,200 @@
+import numpy as np
+from copick.util.uri import resolve_copick_objects
+
+
+def tomogram(run, voxel_size: float = 10, algorithm: str = "wbp", raise_error: bool = False, verbose=True):
+    """
+    Reads a tomogram from a Copick run.
+
+    Parameters:
+    -----------
+    run: copick.Run
+    voxel_size: float
+    algorithm: str
+    raise_error: bool
+    verbose: bool
+    Returns:
+    --------
+    vol: np.ndarray - The tomogram.
+    """
+
+    # Get the tomogram from the Copick URI
+    try:
+        uri = f"{algorithm}@{voxel_size}"
+        vol = resolve_copick_objects(uri, run.root, "tomogram", run_name=run.name)
+        return vol[0].numpy()
+    except Exception as err:  # Report which orbject is missing
+        # Try to resolve the tomogram using the Copick URI
+        voxel_spacing_obj = run.get_voxel_spacing(voxel_size)
+
+        if voxel_spacing_obj is None:
+            # Query Avaiable Voxel Spacings
+            availableVoxelSpacings = [tomo.voxel_size for tomo in run.voxel_spacings]
+
+            # Report to the user which voxel spacings they can use
+            message = (
+                f"[Warning] No tomogram found for {run.name} with uri: {uri}\n"
+                f"Available voxel sizes are: {', '.join(map(str, availableVoxelSpacings))}"
+            )
+            if raise_error:
+                raise ValueError(message) from err
+            elif verbose:
+                print(message)
+            return None
+
+        tomogram = voxel_spacing_obj.get_tomogram(algorithm)
+        if tomogram is None:
+            # Get available algorithms
+            availableAlgorithms = [tomo.tomo_type for tomo in run.get_voxel_spacing(voxel_size).tomograms]
+
+            # Report to the user which algorithms are available
+            message = (
+                f"[Warning] No tomogram found for {run.name} with uri: {uri}\n"
+                f"Available algorithms @{voxel_size}A are: {', '.join(availableAlgorithms)}"
+            )
+            if raise_error:
+                raise ValueError(message) from err
+            elif verbose:
+                print(message)
+            return None
+
+
+def segmentation(run, voxel_spacing: float, name: str, user_id=None, session_id=None, raise_error=False, verbose=True):
+    """
+    Reads a segmentation from a Copick run.
+
+    Parameters:
+    -----------
+    run: copick.Run
+    voxel_spacing: float
+    name: str
+    user_id: str
+    session_id: str
+    raise_error: bool
+    verbose: bool
+    Returns:
+    --------
+    seg: np.ndarray - The segmentation.
+    """
+
+    # Construct the Target URI
+    if session_id is None and user_id is None:
+        uri = f"{name}@{voxel_spacing}"
+    elif session_id is None:
+        uri = f"{name}:{user_id}@{voxel_spacing}"
+    else:
+        uri = f"{name}:{user_id}/{session_id}@{voxel_spacing}"
+
+    # Try to resolve the segmentation using the Copick URI
+    try:
+        segs = resolve_copick_objects(uri, run.root, "segmentation", run_name=run.name)
+        return segs[0].numpy()
+    except Exception as err:
+        # Force the voxel spacing to be a float
+        voxel_spacing = float(voxel_spacing)
+
+        # Get all available segmentations with their metadata
+        available_segs = run.get_segmentations(voxel_size=voxel_spacing)
+
+        if len(available_segs) == 0:
+            available_segs = run.get_segmentations()
+            message = (
+                f"No segmentation found for URI: {uri}\n"
+                f"Available segmentations avaiable w/following voxel sizes: {', '.join(map(str, [s.voxel_size for s in available_segs]))}"
+            )
+        else:
+            seg_info = [(s.name, s.user_id, s.session_id) for s in available_segs]
+
+            # Format the information for display
+            seg_details = [f"(name: {name}, user_id: {uid}, session_id: {sid})" for name, uid, sid in seg_info]
+
+            message = (
+                f"\nNo segmentation at {voxel_spacing} A found matching:\n"
+                f"  name: {name}, user_id: {user_id}, session_id: {session_id}\n"
+                f"Available segmentations in {run.name} are:\n  " + "\n  ".join(seg_details)
+            )
+        if raise_error:
+            raise ValueError(message) from err
+        elif verbose:
+            print(message)
+        else:
+            return None
+
+
+def coordinates(
+    run,  # CoPick run object containing the segmentation data
+    name: str,  # Name of the object or protein for which coordinates are being extracted
+    user_id: str,  # Identifier of the user that generated the picks
+    session_id: str = None,  # Identifier of the session that generated the picks
+    voxel_size: float = 10,  # Voxel size of the tomogram, used for scaling the coordinates
+    raise_error: bool = False,
+    verbose: bool = True,
+):
+    """
+    Reads the coordinates of the picks from a Copick run.
+
+    Parameters:
+    -----------
+    run: copick.Run
+    name: str
+    user_id: str
+    session_id: str
+    voxel_size: float
+    raise_error: bool
+    verbose: bool
+
+    Returns:
+    --------
+    coordinates: np.ndarray - The 3D coordinates of the picks in voxel space.
+    """
+    # Retrieve the pick points associated with the specified object and user ID
+    picks = run.get_picks(object_name=name, user_id=user_id, session_id=session_id)
+
+    if len(picks) == 0:
+        # Get all available segmentations with their metadata
+
+        available_picks = run.get_picks()
+        picks_info = [(s.pickable_object_name, s.user_id, s.session_id) for s in available_picks]
+
+        # Format the information for display
+        picks_details = [f"(name: {name}, user_id: {uid}, session_id: {sid})" for name, uid, sid in picks_info]
+
+        message = (
+            f"\nNo picks found matching:\n"
+            f"  name: {name}, user_id: {user_id}, session_id: {session_id}\n"
+            f"Available picks are:\n  " + "\n  ".join(picks_details)
+        )
+        if raise_error:
+            raise ValueError(message)
+        elif verbose:
+            print(message)
+        return None
+
+    elif len(picks) > 1:
+        # Format pick information for display
+        picks_info = [(p.pickable_object_name, p.user_id, p.session_id) for p in picks]
+        picks_details = [f"(name: {name}, user_id: {uid}, session_id: {sid})" for name, uid, sid in picks_info]
+
+        if verbose:
+            print(
+                "[Warning] More than 1 pick is available for the query information."
+                "\nAvailable picks are:\n  " + "\n  ".join(picks_details) + f"\n"
+                f"Defaulting to loading:\n {picks[0]}\n",
+            )
+
+    points = picks[0].points
+
+    # Initialize an array to store the coordinates
+    nPoints = len(picks[0].points)  # Number of points retrieved
+    coordinates = np.zeros([len(picks[0].points), 3])  # Create an empty array to hold the (z, y, x) coordinates
+
+    # Iterate over all points and convert their locations to coordinates in voxel space
+    for ii in range(nPoints):
+        coordinates[ii,] = [
+            points[ii].location.z / voxel_size,  # Scale z-coordinate by voxel size
+            points[ii].location.y / voxel_size,  # Scale y-coordinate by voxel size
+            points[ii].location.x / voxel_size,
+        ]  # Scale x-coordinate by voxel size
+
+    # Return the array of coordinates
+    return coordinates