Create a dataset

File formats

Thunor accepts several file formats containing cell count data from high throughput experiments.

Vanderbilt HTS Core format

Thunor Web can accept annotated (with cell lines, drugs, and concentrations) or unannotated uploads in this format. Annotated files require all the fields in the table below, except those marked as optional. Unannotated files must omit all of cell.line, and "drug" prefixed fields - i.e. the only fields required for unannotated data are upid, well, cell.count and time.

If uploading unannotated data, plates can be annotated with cell lines, drugs and concentrations using Thunor Web's plate mapper.

Tab-delimited format, UTF-8 character encoding. Fields may be in any order. Extra columns may be present but will be ignored. The plate size will be detected based on the highest well number of the plate.

Field Data type Description
upid string Unique plate ID (only needs to be unique within a dataset)
well string Well position on a plate, 1 character and 2 numbers, e.g. A01
cell.count non-negative int Count of cells in specified well
time non-negative float Time in hours
cell.line string Cell line name
drug1 string Drug 1 name
drug1.conc non-negative float Drug 1 concentration (molar)
drug1.units string Must be M
expt.id string Experiment ID (optional)
expt.date string Experiment date yyyy-mm-dd format (optional)
drug2, drug2.conc, drug2.units Defined analogously to drug1 fields

Notes

Any other columns may be present but will be ignored.

Thunor HDF5 format

Files downloaded from Thunor, or from the Thunor Python package, in HDF5 format.

IncuCyte Zoom format

Thunor can also read files from the IncuCyte system from Essen BioScience. The IncuCyte Zoom software should be used to export a fluorescence marker proxy for cell counts. By default, the filename will be used as the plate name, unless a value is present in the Label: field.

The export can either contain one unified quantification per well (which by default is the median), in which case the header looks like the first example below, or each image can be exported separately, like the second example below. In the latter case, a unified score for each well is calculated as the sum of the values across all images at each time point.

Label:

Date Time   Elapsed A1  B1  C1 ...

In the above example, one count (fluorescence readout) is specified per well.

Label:

Date Time   Elapsed A1.Image1 A1.Image2 B1.Image1 B1.Image2 ...

Process

To begin, click Create Dataset on the home page, or using the icon in the menu at the top of the page. You'll need to be logged in to create a dataset.

  1. Give the dataset a name, and click Next.
  2. Drag and drop cell count files into the marked area, or alternatively use the Browse button to locate files on your computer.
  3. The upload will start automatically. This process may take several minutes, depending on the size of the files.
  4. Click Proceed to Plate Mapper. See the plate mapper documentation for more detail on the next step.