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feat: Add Vi-Cell XR single-sample report format support #1222

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Merged
nathan-stender merged 1 commit into from
Jun 3, 2026
Merged

feat: Add Vi-Cell XR single-sample report format support #1222

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112 changes: 106 additions & 6 deletions src/allotropy/parsers/beckman_vi_cell_xr/vi_cell_xr_reader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,8 +3,9 @@
from dataclasses import dataclass
from io import StringIO
import re
from typing import Any
from typing import Any, ClassVar

import openpyxl
import pandas as pd

from allotropy.named_file_contents import NamedFileContents
Expand Down Expand Up @@ -33,12 +34,34 @@ class ViCellData:
version: XrVersion


def _is_report_format(named_file_contents: NamedFileContents) -> bool:
"""Detect the single-sample report format by checking for key-value layout."""
if named_file_contents.extension not in ("xls", "xlsx"):
return False
try:
wb = openpyxl.load_workbook(
named_file_contents.get_bytes_stream(), read_only=True, data_only=True
)
ws = wb[wb.sheetnames[0]]
rows = list(ws.iter_rows(min_row=4, max_row=4, values_only=True))
wb.close()
if rows and rows[0][0] == "Sample ID":
return True
except Exception:
return False
return False


def create_reader_data(named_file_contents: NamedFileContents) -> ViCellData:
reader: ViCellXRReader | ViCellXRTXTReader = (
ViCellXRTXTReader(named_file_contents)
if named_file_contents.extension == "txt"
else ViCellXRReader(named_file_contents)
)
if named_file_contents.extension == "txt":
reader: ViCellXRReader | ViCellXRTXTReader | ViCellXRReportReader = (
ViCellXRTXTReader(named_file_contents)
)
elif _is_report_format(named_file_contents):
named_file_contents.contents.seek(0)
reader = ViCellXRReportReader(named_file_contents)
else:
reader = ViCellXRReader(named_file_contents)
return ViCellData(reader.data, reader.serial_number, reader.version)


Expand Down Expand Up @@ -127,6 +150,83 @@ def _get_file_info(self) -> SeriesData:
return SeriesData(info)


class ViCellXRReportReader:
"""Reader for the single-sample report format exported by Vi-CELL XR 2.04."""

data: list[SeriesData]
serial_number: str | None
version: XrVersion

RESULTS_FIELDS: ClassVar[dict[str, int]] = {
"Total cells": 9,
"Viable cells": 10,
"Viability (%)": 11,
"Total cells/ml (x10^6)": 12,
"Viable cells/ml (x10^6)": 13,
"Avg. diam. (microns)": 14,
"Avg. circ.": 15,
"Images": 16,
"Average cells / image": 17,
"Avg. background intensity": 18,
}

SETTINGS_FIELDS: ClassVar[dict[str, int]] = {
"Cell type": 9,
"Minimum diameter (microns)": 10,
"Maximum diameter (microns)": 11,
"Minimum circularity": 12,
"Dilution factor": 13,
"Cell brightness (%)": 14,
"Cell sharpness": 15,
"Viable cell spot brightness (%)": 16,
"Viable cell spot area (%)": 17,
"Decluster degree": 18,
"Aspirate cycles": 19,
"Trypan blue mixing cycles": 20,
}

def __init__(self, named_file_contents: NamedFileContents) -> None:
wb = openpyxl.load_workbook(
named_file_contents.get_bytes_stream(), read_only=True, data_only=True
)
ws = wb[wb.sheetnames[0]]
self.rows = list(ws.iter_rows(values_only=True))
wb.close()

self.version = _get_file_version(str(self.rows[0][0]))
self.serial_number = None
self.data = self._read_data()

def _read_data(self) -> list[SeriesData]:
data: dict[str, Any] = {}

data["Sample ID"] = self.rows[3][2]
data["File name"] = self.rows[4][2]
data[DATE_HEADER] = self.rows[5][2]
comment = self.rows[6][2] if len(self.rows) > 6 else None
if comment:
data["Comment"] = comment

for field, row_idx in self.RESULTS_FIELDS.items():
if row_idx < len(self.rows):
val = self.rows[row_idx][3]
if val is not None:
data[field] = val

for field, row_idx in self.SETTINGS_FIELDS.items():
if row_idx < len(self.rows):
val = self.rows[row_idx][8]
if val is not None:
data[field] = val

series = pd.Series(data)
series[DATE_HEADER] = pd.to_datetime(
series[DATE_HEADER],
format="%d %b %Y %I:%M:%S %p",
)
return [SeriesData(series)]


class ViCellXRTXTReader:
data: list[SeriesData]
serial_number: str | None
Expand Down
120 changes: 120 additions & 0 deletions tests/parsers/beckman_vi_cell_xr/testdata/v2.04/Beckman_Vi-Cell-XR_report_format.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,120 @@
{
"$asm.manifest": "http://purl.allotrope.org/manifests/cell-counting/REC/2024/09/cell-counting.manifest",
"cell counting aggregate document": {
"data system document": {
"ASM file identifier": "Beckman_Vi-Cell-XR_report_format.json",
"data system instance identifier": "N/A",
"ASM converter name": "allotropy_beckman_coulter_vi_cell_xr",
"ASM converter version": "0.1.134",
"file name": "Beckman_Vi-Cell-XR_report_format.xlsx",
"software name": "Vi-Cell XR",
"software version": "2.04",
"UNC path": "tests/parsers/beckman_vi_cell_xr/testdata/v2.04/Beckman_Vi-Cell-XR_report_format.xlsx"
},
"device system document": {
"device identifier": "N/A",
"model number": "Vi-Cell XR"
},
"cell counting document": [
{
"measurement aggregate document": {
"measurement document": [
{
"device control aggregate document": {
"device control document": [
{
"detection type": "brightfield",
"device type": "brightfield imager (cell counter)",
"custom information document": {
"Trypan blue mixing cycles": 3.0,
"Aspirate cycles": 1.0
}
}
]
},
"measurement identifier": "BECKMAN_VI_CELL_XR_TEST_ID_0",
"measurement time": "2026-05-11T14:59:27+00:00",
"processed data aggregate document": {
"processed data document": [
{
"data processing document": {
"cell type processing method": "Default",
"cell density dilution factor": {
"value": 1.0,
"unit": "(unitless)"
},
"minimum cell diameter setting": {
"value": 5.0,
"unit": "µm"
},
"maximum cell diameter setting": {
"value": 50.0,
"unit": "µm"
},
"custom information document": {
"Decluster degree": "Medium",
"Viable cell spot area (%)": 5.0,
"Minimum circularity": 0.0,
"Cell brightness (%)": 85.0,
"Viable cell spot brightness (%)": 75.0,
"Cell sharpness": 100.0
}
},
"viability (cell counter)": {
"value": 86.99453735351562,
"unit": "%"
},
"total cell density (cell counter)": {
"value": 0.9703072143554687,
"unit": "10^6 cells/mL"
},
"viable cell density (cell counter)": {
"value": 0.8441272808074951,
"unit": "10^6 cells/mL"
},
"average total cell diameter": {
"value": 16.80272565612793,
"unit": "µm"
},
"total cell count": {
"value": 915,
"unit": "cell"
},
"viable cell count": {
"value": 796,
"unit": "cell"
},
"average total cell circularity": {
"value": 0.6407691074371338,
"unit": "(unitless)"
},
"custom information document": {
"Avg. background intensity": 202.89999389648438,
"Average cells / image": 18.299999237060547
}
}
]
},
"sample document": {
"sample identifier": "7B"
},
"image aggregate document": {
"image document": [
{
"custom information document": {
"Images": 50.0
}
}
]
}
}
],
"custom information document": {
"experimental data identifier": "C:\\ViCELLXR\\Data\\7B.txt"
}
},
"analyst": "Vi-Cell XR"
}
]
}
}
Binary file added tests/parsers/beckman_vi_cell_xr/testdata/v2.04/Beckman_Vi-Cell-XR_report_format.xlsx
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