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 float | Count of cells in specified well (or a fluorescence proxy for cell count) |
| 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.
- Give the dataset a name, and click Next.
- Drag and drop cell count files into the marked area, or alternatively use the Browse button to locate files on your computer.
- The upload will start automatically. This process may take several minutes, depending on the size of the files.
- Click Proceed to Plate Mapper. See the plate mapper documentation for more detail on the next step.