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Wells

The Wells section includes the WellLocation, WellLabel, CellType, and CellDiameter columns. When the Wells section is populated, the WellLabel and WellLocation columns are required. When the Wells section is unpopulated or the user does not include a run manifest in run planning, the instrument defaults the well label of every well to be that well's location (e.g., A1).

Columns​

ColumnValue
WellLocationThe location of the well on the flow cell. Valid values for this column are a letter and number combination, where the letter is between A-F and the number is between 1-2. A 1-well consumable only contains the well A1. The user can specify multiple well locations in a single row using a "+" to link well locations, e.g. A1+A2+B1.
WellLabelThe label for the well(s) specified in the well location column. Each label can include 1–64 case-sensitive alphanumeric characters, hyphens (-), and underscores (_).
CellTypeThe cell type in the well(s). This determines the segmentation model used onboard the instrument. The following values are valid, agnostic to spaces, capitalization, or hyphens: HeLa​, HUVEC​, PC-3​, Hep-G2​, MCF-7​, HCT-116​, or Other. Multiple cell types can be included using a "+" to link them for a co-culture. When no cell type is entered, the system defaults to a generalized segmentation model.
CellDiameterThe predicted diameter of the cell line in the well(s) in microns. Valid values for this field are numeric values above 15. This field is used to improve onboard cell segmentation performance when the well contains a cell type of "Other." Otherwise, the segmentation model for the specified cell type is used.

Custom Sample-Level Metadata​

An optional addition to the Samples section, custom columns specify additional key-value metadata for samples. Custom columns must meet the following requirements:

  • Each custom column name is unique, including case-sensitive variations.
  • A custom column cannot have the same name as a required column.
  • When a sample name is repeated, each corresponding value in the custom column must match exactly.
  • The key character limit is 1–64. Valid characters include lower- and upper-case letters, numbers, hyphens, and underscores.
  • The value character limit is 0–255 ASCII characters.

Well Specification Examples​

The following examples show how to construct a manifest for specific use cases.

Defining Cell Type for a 1-Well Flow Cell​

  • Defining HeLa as the cell type for a culture in a 1-well flow cell
[Wells],,,,
WellLocation,WellLabel,CellType
A1,Well_One_Label,HeLa

Adding Custom Metadata for a 12-well Flow Cell​

  • Add a custom column, Custom_Metadata, with metadata Well_1_metadata, Well_2_metadata, and Well_3_metadata, and so on.
[Wells],,,,
WellLocation,WellLabel,CellType,CellDiameter,Custom
A1,Well_1_Label,HeLa,,Well_1_metadata
A2,Well_2_Label,HeLa,,Well_2_metadata
B1,Well_3_Label,HeLa,,Well_3_metadata
B2,Well_4_Label,HeLa,,Well_4_metadata
C1,Well_5_Label,HeLa,,Well_5_metadata
C2,Well_6_Label,HeLa,,Well_6_metadata
D1,Well_7_Label,HeLa,,Well_7_metadata
D2,Well_8_Label,HeLa,,Well_8_metadata
E1,Well_9_Label,HeLa,,Well_9_metadata
E2,Well_10_Label,HeLa,,Well_10_metadata
F1,Well_11_Label,HeLa,,Well_11_metadata
F2,Well_12_Label,HeLa,,Well_12_metadata

Assigning Information to Multiple Well Locations​

  • Associate a set of well information, including well label, cell type, and cell diameter, to multiple well locations.
[Wells],,,,
WellLocation,WellLabel,CellType,CellDiameter
A1+A2,Well_A_Label,HeLa,
B1+B2,Well_B_Label,Other,30
C1+C2,Well_C_Label,Other,45
D1+D2,Well_D_Label,Jurkat,
E1+E2,Well_E_Label,Huvec,
F1+F2,Well_F_Label,HeLa+Jurkat,
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