neuralib.atlas.brainrender.probe_rst

class neuralib.atlas.brainrender.probe_rst.ProbeReconstructor[source]

DESCRIPTION: str = 'For probe(s) track reconstruction': parser description.

implant_depth: int: implant depth in um

dye_label_only: bool: only show the histology dye parts

csv_file: Path

Example:

┌───────────────────────────────────┬─────────┬─────────────┬─────────────┬─────────────┬─────────┐
│ name                              ┆ acronym ┆ AP_location ┆ DV_location ┆ ML_location ┆ avIndex │
│ ---                               ┆ ---     ┆ ---         ┆ ---         ┆ ---         ┆ ---     │
│ str                               ┆ str     ┆ f64         ┆ f64         ┆ f64         ┆ i64     │
╞═══════════════════════════════════╪═════════╪═════════════╪═════════════╪═════════════╪═════════╡
│ Primary visual area layer 6a      ┆ VISp6a  ┆ -3.81       ┆ 1.92        ┆ -3.12       ┆ 191     │
│ optic radiation                   ┆ or      ┆ -4.08       ┆ 2.33        ┆ -3.12       ┆ 1217    │
│ Posterolateral visual area layer… ┆ VISpl6a ┆ -4.28       ┆ 2.29        ┆ -3.12       ┆ 198     │
│ Posterolateral visual area layer… ┆ VISpl5  ┆ -4.52       ┆ 2.17        ┆ -3.12       ┆ 197     │
│ Subiculum                         ┆ SUB     ┆ -3.93       ┆ 4.36        ┆ -3.3        ┆ 536     │
│ Entorhinal area medial part dors… ┆ ENTm5   ┆ -4.19       ┆ 4.39        ┆ -3.3        ┆ 515     │
│ Entorhinal area medial part dors… ┆ ENTm2   ┆ -4.44       ┆ 4.39        ┆ -3.3        ┆ 510     │
│ Entorhinal area medial part dors… ┆ ENTm1   ┆ -4.66       ┆ 4.29        ┆ -3.3        ┆ 509     │
└───────────────────────────────────┴─────────┴─────────────┴─────────────┴─────────────┴─────────┘

plane_type: Literal['coronal', 'sagittal', 'transverse']: cutting orientation. Assume if multiple shanks were inserted along the AP axis, then do the sagittalslicing, if inserted along the ML axis, then do the coronal slicing

raw: DataFrame: raw csv file

data: DataFrame: sorted data based on plane_type

load()[source]: Overwrite by children

property number_shanks: int

class ShanksTrack[source]

shank object

Dimension parameters:

S = number of shanks

P = number of sample points after interpolated reconstruction

rst: ProbeReconstructor: ProbeReconstructor

shanks: list[ndarray]: length S of Array[float, [P, 3]], with ap, dv, ml

with_theoretical(interval=250)[source]

theoretical track based on implantation depth / angle

Parameters:: interval (int) – istance (um) relative to the specific shank. e.g., NeuroPixel 2.0 = 250 * x
Returns:: ShanksTrack
Return type:: Self

__init__(rst, shanks)

Parameters:

rst (ProbeReconstructor)
shanks (list[ndarray])

Return type:

None

get_probe_object()[source]

Return type:: ShanksTrack

infer_probe_index(df)[source]

probe in correct order index

Parameters:: df (DataFrame) – raw csv file
Returns:: dataframe with probe and probe_idx fields.
Return type:: DataFrame

Example:

┌───────────────────────────────────┬─────────┬─────────────┬─────────────┬─────────────┬─────────┬───────────────┬───────────┐
│ name                              ┆ acronym ┆ AP_location ┆ DV_location ┆ ML_location ┆ avIndex ┆ probe         ┆ probe_idx │
│ ---                               ┆ ---     ┆ ---         ┆ ---         ┆ ---         ┆ ---     ┆ ---           ┆ ---       │
│ str                               ┆ str     ┆ f64         ┆ f64         ┆ f64         ┆ i64     ┆ str           ┆ i64       │
╞═══════════════════════════════════╪═════════╪═════════════╪═════════════╪═════════════╪═════════╪═══════════════╪═══════════╡
│ Primary visual area layer 6a      ┆ VISp6a  ┆ -3.81       ┆ 1.92        ┆ -3.12       ┆ 191     ┆ dorsal_label  ┆ 1         │
│ Subiculum                         ┆ SUB     ┆ -3.93       ┆ 4.36        ┆ -3.3        ┆ 536     ┆ ventral_label ┆ 1         │
│ optic radiation                   ┆ or      ┆ -4.08       ┆ 2.33        ┆ -3.12       ┆ 1217    ┆ dorsal_label  ┆ 2         │
│ Entorhinal area medial part dors… ┆ ENTm5   ┆ -4.19       ┆ 4.39        ┆ -3.3        ┆ 515     ┆ ventral_label ┆ 2         │
│ Posterolateral visual area layer… ┆ VISpl6a ┆ -4.28       ┆ 2.29        ┆ -3.12       ┆ 198     ┆ dorsal_label  ┆ 3         │
│ Entorhinal area medial part dors… ┆ ENTm2   ┆ -4.44       ┆ 4.39        ┆ -3.3        ┆ 510     ┆ ventral_label ┆ 3         │
│ Posterolateral visual area layer… ┆ VISpl5  ┆ -4.52       ┆ 2.17        ┆ -3.12       ┆ 197     ┆ dorsal_label  ┆ 4         │
│ Entorhinal area medial part dors… ┆ ENTm1   ┆ -4.66       ┆ 4.29        ┆ -3.3        ┆ 509     ┆ ventral_label ┆ 4         │
└───────────────────────────────────┴─────────┴─────────────┴─────────────┴─────────────┴─────────┴───────────────┴───────────┘

isin_brain(shank)[source]

determine if the probe points are in the brain

Parameters:: shank (ndarray) – Array[float, [P, 3]]
Returns:
Return type:: ndarray

crop_outside_brain(shank, distance, dv_value=None)[source]

crop the probe after doing the extension

Parameters:

shank (ndarray) – Array[float, [P, 3]]
distance (float) – depth of insertion (might with an angle, in um). mostly records during the implantation use the depth value that used while implantation to cutoff the bottom line.
dv_value (int | None) – if None, plot the probe if its in the brain if int type, plot the probe if dv larger than this value

Returns:

Return type:

ndarray