Installing requirements

The cell below installs every Python package needed to run this notebook, at fully pinned versions, using uv for fast resolution. In Colab the cell is collapsed by default — click the ▶ button to run it.

# install cell skipped during CI (deps preinstalled into system Python)

⚠️ Restart runtime after install

The install may upgrade packages already loaded in the kernel. Go to Runtime → Restart session, then Run all cells below (skip this install cell on re-run).

# Import the local module containing helper functions specific to Dandiset 001075
import utils_001075

subject_id = "26"
session_id = "20211104-163944"

exclude_labels = ["AMsoL", "AMsoR", "AMso", "AMSoL", "AMSoR", "AmSo"]

segmentation_nwbfile = utils_001075.stream_nwbfile(
    subject_id=subject_id,
    session_id=session_id,
    session_type="segmentation",
)

/opt/hostedtoolcache/Python/3.13.15/x64/lib/python3.13/site-packages/hdmf/spec/namespace.py:484: UserWarning: Schema conflict(s) detected in namespace 'ndx-microscopy': 
 ndx-microscopy defines Microscope.model as an attribute (dtype: text) while the core schema defines it as a link to DeviceModel.
ndx-microscopy defines MicroscopyLightSource.model as an attribute (dtype: text) while the core schema defines it as a link to DeviceModel. 
This may cause compatibility issues. Please update the extension version if possible or install an older version of the core schema that is compatible.
  self._check_namespace_conflicts(extension_ns_name=ns_name,
/opt/hostedtoolcache/Python/3.13.15/x64/lib/python3.13/site-packages/hdmf/spec/namespace.py:484: UserWarning: Schema conflict(s) detected in namespace 'ndx-patterned-ogen': 
 ndx-patterned-ogen defines SpatialLightModulator2D.model as an attribute (dtype: text) while the core schema defines it as a link to DeviceModel.
ndx-patterned-ogen defines SpatialLightModulator3D.model as an attribute (dtype: text) while the core schema defines it as a link to DeviceModel.
ndx-patterned-ogen defines LightSource.model as an attribute (dtype: text) while the core schema defines it as a link to DeviceModel. 
This may cause compatibility issues. Please update the extension version if possible or install an older version of the core schema that is compatible.
  self._check_namespace_conflicts(extension_ns_name=ns_name,

/opt/hostedtoolcache/Python/3.13.15/x64/lib/python3.13/site-packages/hdmf/build/objectmapper.py:1399: UserWarning: Device.model was detected as a string, but NWB 2.9 specifies Device.model as a link to a DeviceModel. Remapping "ORPHEUS amplifier and PHAROS laser" to a new DeviceModel.
  override = self.__get_override_carg(argname, builder, manager)

utils_001075.plot_waterfall(
    segmentation_nwbfile=segmentation_nwbfile,
    exclude_labels=exclude_labels,
)