Create a cell screening manifest

Learn how to create a manifest from a template or manually, and complete the Wells and Run Values sections.

A cell screening run manifest file includes the following sections. Each section starts with a bracketed section heading that is followed by a row of column headings. Section and column headings are case insensitive. All subsequent rows list metadata for the section.

Section	Purpose
Wells	Specifies well information for cell screening primary analysis
Run Values	Adds custom information for user annotations

Create the file

Build the manifest manually in a spreadsheet editor, or download and edit a run manifest template. Both paths produce the same manifest.

To build the file manually, copy the following into a spreadsheet, and then add your well and run-value metadata. In Excel, save the file with File > Save As and choose the CSV UTF-8 (Comma delimited) format.

[RunValues]
KeyName, Value
[Wells]
WellLocation, WellLabel, CellType, CellDiameter

Add metadata to the Run Values and Wells sections as needed, and then save the finished run manifest as a CSV UTF-8 file.

• Allowed characters in file name are are letters, numbers, dash, dot, parentheses, and underscore.
• Do not include spaces in the file name.

Run manifest templates

Every template contains minimal metadata that uses default settings, and example wells.

Downloadable Template	AVITI OS Version
Single Well Run Manifest Template	v3.0.0 and later
12-Well Run Manifest Template	v3.0.0 and later
12-Well OPS/MPS Run Manifest Template (Target to Cell Assignment)	v3.4.0 and later
48-Well Run Manifest Template	v3.4.0 and later

For a run that uses target cell assignment, you also need a target cell assignment manifest. See Target cell assignment manifest templates.

Wells section

The Wells section defines well specific metadata, such as naming the well or assigning what segmenttion model to apply based on cell type. When the Wells section is populated, the WellLabel and WellLocation columns are required. When you do not include a run manifest in run planning, the default well label of every well is the location of the well, for example A1.

Columns

Column	Constraints	Definition	Allowed Values
WellLocation	Required	The 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–L and the number is between 1–4. Use + to link multiple locations.
WellLabel	Required	The label for the well(s) that are specified in the well location column.	1–64 case-sensitive alphanumeric characters, hyphens (-), and underscores (_)
CellType	Optional	The cell type in the well(s). This determines the segmentation model that is used onboard the instrument.	A supported cell line or tissue type, or Other. See Cell type values
CellDiameter	Optional	The predicted diameter, in pixels, of the cell line in the well(s). The conversion from pixels to diameter is size (µm) = size (pixels) * 0.48 (µm/pixel). 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.	Numeric values above 15
TargetSiteNames	Optional	(For Cytos™ OPS or MPS and only for use with a Target Cell Assignment manifest) If left blank and the run has target to cell assignment, then it is assumed that all targets are present in all wells. To add multiple targets to one well, use + to separate targets.	Valid values are None, blank (empty), or target site names that are composed of 1–64 case-sensitive alphanumeric characters, hyphens (-), and underscores (_)

Cell type values

The instrument uses CellType to select the onboard segmentation model. The following values are valid:

HeLa, HEK293, HUVEC, PC3, Jurkat, HepG2, MCF7, HCT116, SHSY5Y, PBMC, Fibroblast, IPSCWT, and Other

Values are case insensitive, and the instrument ignores spaces and hyphens. HepG2, Hep-G2, and hep g2 are therefore equivalent.

To assign more than one cell type to a well, separate the values with +, as shown in Assigning information to multiple well locations.

Custom well-level metadata

Custom columns are an optional addition to the Wells section and specify additional key-value metadata for wells. Custom columns must meet the following requirements:

• Each custom column name is unique and includes case-sensitive variations.
• A custom column cannot have the same name as a required column.
• When a well label 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

Define 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

Add a custom column, Custom_Metadata, and give each well its own value. Include one row per well in the flow cell:

[Wells],,,,
WellLocation,WellLabel,CellType,CellDiameter,Custom_Metadata
A1,Well_1_Label,HeLa,,Well_1_metadata
B1,Well_2_Label,HeLa,,Well_2_metadata
C1,Well_3_Label,HeLa,,Well_3_metadata
...

For prefilled 1-well, 12-well, and 48-well layouts, download a run manifest template.

Assigning information to multiple well locations

For multiple well locations, associate a set of well information and include the well label, cell type, and cell diameter:

[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,

Adding TargetSiteNames to a 12-well target cell assignment manifest

For Cytos OPS or MPS runs with a Target Cell Assignment manifest, add a TargetSiteNames column with targets 1_FirstTarget for a well with a single target, or 1_FirstTarget+2_SecondTarget for a well with multiple targets:

[Wells],,,,
WellLocation,WellLabel,CellType,TargetSiteNames,Custom_Metadata
A1,thisiswell_1,Hela,1_FirstTarget,
A2,thisiswell_2,Hela,1_FirstTarget,
B1,thisiswell_3,Hela,1_FirstTarget,
B2,thisiswell_4,Hela,1_FirstTarget,
C1,thisiswell_5,Hela,1_FirstTarget,
C2,thisiswell_6,Hela,1_FirstTarget+2_SecondTarget,
...

Run values section

The [Run Values] section includes KeyName and Value columns that record any arbitrary metadata for historical or analysis purposes. The metadata are run-level key-value pairs, which the software transfers with the run but does not add to a database or otherwise track. If you include a duplicate key, the last recorded value is used.

Columns

Column	Constraints	Description	Allowed Values
KeyName	Required	The key name defines the key-value of the metadata pair.	1–64 alphanumeric characters, hyphens, and underscores
Value	Required	A variable that belongs to the key.	0–16,384 ASCII characters

Reserved keys

The following key is reserved for special purpose data. Use any other key name for your own annotations.

Key	Value
ExternalID	An external identifier to associate with the run

Run value specification examples

The [Run Values] section accepts any number of key-value pairs, so record every annotation for a run in a single section. The following example associates an external identifier with the run and records cell culture and staining details for a cell screening experiment:

[RunValues],
KeyName,Value
ExternalID,14f107c2-ffeb-4e07-b62a-4704bb053a68
CellPassageNumber,12
SeedingDensity,5000-cells-per-well
TreatmentCompound,Nocodazole
FixationDate,2026-02-18
AntibodyLot,AB-4471-02

Apart from ExternalID, key names are arbitrary. Choose names that describe your experiment, and use the same names across runs so that you can compare annotations later.

Note:

Run values are annotations only. Cells2Stats does not read them, and they do not change how the instrument or analysis processes a run. To change analysis behavior, use the Wells section or the Cells2Stats CLI options.