Skills › Knowledge Work Plugins › instrument-data-to-allotrope › supported_instruments.md

supported_instruments.md

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1# Supported Instruments

Supported Instruments

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3## What Can This Skill Convert?

5**Any instrument data that maps to an Allotrope schema can be converted.** The skill uses a tiered parsing approach:

71. **Native allotropy parsers** (listed below) - Highest fidelity, validated against vendor-specific formats

82. **Flexible fallback parser** - Handles any tabular data (CSV, Excel, TXT) by mapping columns to ASM fields

93. **PDF extraction** - Extracts tables from PDFs, then applies flexible parsing

11If your instrument isn't listed below, the skill can still convert it as long as your data contains recognizable measurement fields (sample IDs, values, units, timestamps, etc.) that map to an ASM technique schema.

13---

What Can This Skill Convert?

Any instrument data that maps to an Allotrope schema can be converted. The skill uses a tiered parsing approach:

Native allotropy parsers (listed below) - Highest fidelity, validated against vendor-specific formats
Flexible fallback parser - Handles any tabular data (CSV, Excel, TXT) by mapping columns to ASM fields
PDF extraction - Extracts tables from PDFs, then applies flexible parsing

If your instrument isn't listed below, the skill can still convert it as long as your data contains recognizable measurement fields (sample IDs, values, units, timestamps, etc.) that map to an ASM technique schema.

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15## Instruments with Native Allotropy Parsers

17The following instruments have optimized parsers in the allotropy library with their Vendor enum values.

Instruments with Native Allotropy Parsers

The following instruments have optimized parsers in the allotropy library with their Vendor enum values.

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19## Cell Counting

21| Instrument | Vendor Enum | File Types |

22|------------|-------------|------------|

23| Beckman Coulter Vi-CELL BLU | `BECKMAN_VI_CELL_BLU` | .csv |

24| Beckman Coulter Vi-CELL XR | `BECKMAN_VI_CELL_XR` | .txt, .xls, .xlsx |

25| ChemoMetec NucleoView NC-200 | `CHEMOMETEC_NUCLEOVIEW` | .xlsx |

26| ChemoMetec NC-View | `CHEMOMETEC_NC_VIEW` | .xlsx |

27| Revvity Matrix | `REVVITY_MATRIX` | .csv |

Cell Counting

Instrument	Vendor Enum	File Types
Beckman Coulter Vi-CELL BLU	`BECKMAN_VI_CELL_BLU`	.csv
Beckman Coulter Vi-CELL XR	`BECKMAN_VI_CELL_XR`	.txt, .xls, .xlsx
ChemoMetec NucleoView NC-200	`CHEMOMETEC_NUCLEOVIEW`	.xlsx
ChemoMetec NC-View	`CHEMOMETEC_NC_VIEW`	.xlsx
Revvity Matrix	`REVVITY_MATRIX`	.csv

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29## Spectrophotometry (UV-Vis)

31| Instrument | Vendor Enum | File Types |

32|------------|-------------|------------|

33| Thermo Fisher NanoDrop One | `THERMO_FISHER_NANODROP_ONE` | .csv, .xlsx |

34| Thermo Fisher NanoDrop Eight | `THERMO_FISHER_NANODROP_EIGHT` | .tsv, .txt |

35| Thermo Fisher NanoDrop 8000 | `THERMO_FISHER_NANODROP_8000` | .csv |

36| Unchained Labs Lunatic | `UNCHAINED_LABS_LUNATIC` | .csv, .xlsx |

37| Thermo Fisher Genesys 30 | `THERMO_FISHER_GENESYS30` | .csv |

Spectrophotometry (UV-Vis)

Instrument	Vendor Enum	File Types
Thermo Fisher NanoDrop One	`THERMO_FISHER_NANODROP_ONE`	.csv, .xlsx
Thermo Fisher NanoDrop Eight	`THERMO_FISHER_NANODROP_EIGHT`	.tsv, .txt
Thermo Fisher NanoDrop 8000	`THERMO_FISHER_NANODROP_8000`	.csv
Unchained Labs Lunatic	`UNCHAINED_LABS_LUNATIC`	.csv, .xlsx
Thermo Fisher Genesys 30	`THERMO_FISHER_GENESYS30`	.csv

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39## Plate Readers (Multi-mode, Absorbance, Fluorescence)

41| Instrument | Vendor Enum | File Types |

42|------------|-------------|------------|

43| Molecular Devices SoftMax Pro | `MOLDEV_SOFTMAX_PRO` | .txt |

44| PerkinElmer EnVision | `PERKIN_ELMER_ENVISION` | .csv |

45| Agilent Gen5 (BioTek) | `AGILENT_GEN5` | .xlsx |

46| Agilent Gen5 Image | `AGILENT_GEN5_IMAGE` | .xlsx |

47| BMG MARS (CLARIOstar) | `BMG_MARS` | .csv, .txt |

48| BMG LabTech Smart Control | `BMG_LABTECH_SMART_CONTROL` | .csv |

49| Thermo SkanIt | `THERMO_SKANIT` | .xlsx |

50| Revvity Kaleido | `REVVITY_KALEIDO` | .csv |

51| Tecan Magellan | `TECAN_MAGELLAN` | .xlsx |

Plate Readers (Multi-mode, Absorbance, Fluorescence)

Instrument	Vendor Enum	File Types
Molecular Devices SoftMax Pro	`MOLDEV_SOFTMAX_PRO`	.txt
PerkinElmer EnVision	`PERKIN_ELMER_ENVISION`	.csv
Agilent Gen5 (BioTek)	`AGILENT_GEN5`	.xlsx
Agilent Gen5 Image	`AGILENT_GEN5_IMAGE`	.xlsx
BMG MARS (CLARIOstar)	`BMG_MARS`	.csv, .txt
BMG LabTech Smart Control	`BMG_LABTECH_SMART_CONTROL`	.csv
Thermo SkanIt	`THERMO_SKANIT`	.xlsx
Revvity Kaleido	`REVVITY_KALEIDO`	.csv
Tecan Magellan	`TECAN_MAGELLAN`	.xlsx

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53## ELISA / Immunoassay

55| Instrument | Vendor Enum | File Types |

56|------------|-------------|------------|

57| Molecular Devices SoftMax Pro | `MOLDEV_SOFTMAX_PRO` | .txt |

58| MSD Discovery Workbench | `MSD_WORKBENCH` | .txt |

59| MSD Methodical Mind | `METHODICAL_MIND` | .xlsx |

60| BMG MARS | `BMG_MARS` | .csv, .txt |

ELISA / Immunoassay

Instrument	Vendor Enum	File Types
Molecular Devices SoftMax Pro	`MOLDEV_SOFTMAX_PRO`	.txt
MSD Discovery Workbench	`MSD_WORKBENCH`	.txt
MSD Methodical Mind	`METHODICAL_MIND`	.xlsx
BMG MARS	`BMG_MARS`	.csv, .txt

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62## qPCR / PCR

64| Instrument | Vendor Enum | File Types |

65|------------|-------------|------------|

66| Applied Biosystems QuantStudio | `APPBIO_QUANTSTUDIO` | .xlsx |

67| Applied Biosystems QuantStudio Design & Analysis | `APPBIO_QUANTSTUDIO_DESIGNANALYSIS` | .xlsx, .csv |

68| Bio-Rad CFX Maestro | `BIORAD_CFX_MAESTRO` | .csv, .xlsx |

69| Roche LightCycler | `ROCHE_LIGHTCYCLER` | .txt |

qPCR / PCR

Instrument	Vendor Enum	File Types
Applied Biosystems QuantStudio	`APPBIO_QUANTSTUDIO`	.xlsx
Applied Biosystems QuantStudio Design & Analysis	`APPBIO_QUANTSTUDIO_DESIGNANALYSIS`	.xlsx, .csv
Bio-Rad CFX Maestro	`BIORAD_CFX_MAESTRO`	.csv, .xlsx
Roche LightCycler	`ROCHE_LIGHTCYCLER`	.txt

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71## Chromatography (HPLC, LC)

73| Instrument | Vendor Enum | File Types |

74|------------|-------------|------------|

75| Waters Empower | `WATERS_EMPOWER` | .xml |

76| Thermo Fisher Chromeleon | `THERMO_FISHER_CHROMELEON` | .xml |

77| Agilent ChemStation | `AGILENT_CHEMSTATION` | .csv |

Chromatography (HPLC, LC)

Instrument	Vendor Enum	File Types
Waters Empower	`WATERS_EMPOWER`	.xml
Thermo Fisher Chromeleon	`THERMO_FISHER_CHROMELEON`	.xml
Agilent ChemStation	`AGILENT_CHEMSTATION`	.csv

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79## Electrophoresis

81| Instrument | Vendor Enum | File Types |

82|------------|-------------|------------|

83| Agilent TapeStation | `AGILENT_TAPESTATION` | .csv |

84| PerkinElmer LabChip | `PERKIN_ELMER_LABCHIP` | .csv |

Electrophoresis

Instrument	Vendor Enum	File Types
Agilent TapeStation	`AGILENT_TAPESTATION`	.csv
PerkinElmer LabChip	`PERKIN_ELMER_LABCHIP`	.csv

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86## Flow Cytometry

88| Instrument | Vendor Enum | File Types |

89|------------|-------------|------------|

90| BD Biosciences FACSDiva | `BD_BIOSCIENCES_FACSDIVA` | .xml |

91| FlowJo | `FLOWJO` | .wsp |

Flow Cytometry

Instrument	Vendor Enum	File Types
BD Biosciences FACSDiva	`BD_BIOSCIENCES_FACSDIVA`	.xml
FlowJo	`FLOWJO`	.wsp

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93## Solution Analysis

95| Instrument | Vendor Enum | File Types |

96|------------|-------------|------------|

97| Roche Cedex BioHT | `ROCHE_CEDEX_BIOHT` | .xlsx |

98| Beckman Coulter Biomek | `BECKMAN_COULTER_BIOMEK` | .csv |

Solution Analysis

Instrument	Vendor Enum	File Types
Roche Cedex BioHT	`ROCHE_CEDEX_BIOHT`	.xlsx
Beckman Coulter Biomek	`BECKMAN_COULTER_BIOMEK`	.csv

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100## Auto-Detection Patterns

101

102The skill attempts to identify instrument type from file contents using these patterns:

103

Auto-Detection Patterns

The skill attempts to identify instrument type from file contents using these patterns:

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104### Vi-CELL BLU

105- Column headers: "Sample ID", "Viable cells (x10^6 cells/mL)", "Viability (%)"

106- File structure: CSV with specific column order

107

Vi-CELL BLU

Column headers: "Sample ID", "Viable cells (x10^6 cells/mL)", "Viability (%)"
File structure: CSV with specific column order

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108### Vi-CELL XR

109- Column headers: "Sample", "Total cells/ml", "Viable cells/ml"

110- Multiple export formats supported

111

Vi-CELL XR

Column headers: "Sample", "Total cells/ml", "Viable cells/ml"
Multiple export formats supported

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112### NanoDrop

113- Column headers: "Sample Name", "Nucleic Acid Conc.", "A260", "A280"

114- 260/280 and 260/230 ratio columns

115

NanoDrop

Column headers: "Sample Name", "Nucleic Acid Conc.", "A260", "A280"
260/280 and 260/230 ratio columns

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116### Plate Readers (General)

117- Well identifiers (A1-H12 pattern)

118- "Plate", "Well", "Sample" columns

119- Block-based structure with metadata headers

120

Plate Readers (General)

Well identifiers (A1-H12 pattern)
"Plate", "Well", "Sample" columns
Block-based structure with metadata headers

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121### ELISA

122- Standard curve data with concentrations

123- OD/absorbance readings

124- Sample/blank/standard classification

125

ELISA

Standard curve data with concentrations
OD/absorbance readings
Sample/blank/standard classification

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126## Using Vendor Enums

127

128```python

129from allotropy.parser_factory import Vendor

130from allotropy.to_allotrope import allotrope_from_file

131

132# List all supported vendors

133for v in Vendor:

134 print(f"{v.name}: {v.value}")

135

136# Convert file

137asm = allotrope_from_file("data.csv", Vendor.BECKMAN_VI_CELL_BLU)

138```

139

Using Vendor Enums

from allotropy.parser_factory import Vendor
from allotropy.to_allotrope import allotrope_from_file

# List all supported vendors
for v in Vendor:
    print(f"{v.name}: {v.value}")

# Convert file
asm = allotrope_from_file("data.csv", Vendor.BECKMAN_VI_CELL_BLU)

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140## Checking Supported Status

141

142```python

143from allotropy.parser_factory import get_parser

144

145# Check if a vendor/file combo is supported

146try:

147 parser = get_parser(Vendor.BECKMAN_VI_CELL_BLU)

148 print("Supported!")

149except Exception as e:

150 print(f"Not supported: {e}")

151```

Checking Supported Status

from allotropy.parser_factory import get_parser

# Check if a vendor/file combo is supported
try:
    parser = get_parser(Vendor.BECKMAN_VI_CELL_BLU)
    print("Supported!")
except Exception as e:
    print(f"Not supported: {e}")

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