Generate data from images
Generation builds the data table from the photo jobs of the experiment and its plate schema. Each well that belongs to a sample becomes a row, each photo adds one or more data columns.
Open the dialog with Generate Data (shown while the experiment has no data) or with Regenerate in the header of the data table.
The dialog lists the jobs selected on the Job selection stage. Choose the options and click Generate Data. The stage shows Generating experiment data... until the table is ready.
Generating again rebuilds the whole table from the photos. Manual edits, applied adjustments and imported data are lost. Export the table first if you need to keep them. Analyses that already ran keep their results.
Generation modes
Generation Mode sets the order of the rows:
| Option | Row order |
|---|---|
| Group by Sample (default) | Rows of one sample go together. Samples are sorted by name, wells inside a sample by row, then column (A1, A2, …, B1, …). |
| Grid Order | All wells by plate position: row A left to right, then row B, and so on. Rows of one sample may be far apart. |
The mode changes only the order of the rows, not their content. Group by Sample is easier to read and to select with the mouse, because the data range of one sample is a single block of rows.
Selected jobs and columns
Each job card shows the photo, its file name, the grid size (rows × columns), the crop type and a status badge.
- OK — the grid of the job fits the plate schema: the sizes are equal, or the photo was cropped by one row and/or column and the crop type says which one (Top, Bottom, Left, Right or a corner). The wells of a cropped photo are matched to the plate by that crop type.
- Invalid — the grid does not fit, for example
Grid mismatch: 2x4 with Uncropped crop. The checkbox is disabled and the job is never used. Fix the grid of the photo job or the plate size.
The summary on the left counts Total Selected, Valid and Invalid
jobs. Only valid jobs are sent: the button shows how many
(Generate Data (2 jobs)). Select All and Clear All change the
selection of all jobs at once.
The select on each card is the calculate type: which data columns the photo adds to the table. The select next to Select All sets the same type for all selected jobs.
| Calculate type | Columns added | Value |
|---|---|---|
| RGB (default) | R, G, B | the three channels |
| Intensity | intensity | (R + G + B) / 3 |
| RG Intensity | rg_intensity | (R + G) / 2 |
| RB Intensity | rb_intensity | (R + B) / 2 |
| GB Intensity | gb_intensity | (G + B) / 2 |
| R | R | red channel only |
| G | G | green channel only |
| B | B | blue channel only |
Columns of different photos appear in the order of the jobs in the experiment. The calculate type is stored in the experiment's job list and saved with the experiment (Save Changes), so the next generation starts with the same choice.
What the values mean
A data value is the colour of one well on one photo:
- When a photo job is processed, Chrometrica measures every cell of the detected grid: it takes the pixels of the cell area and computes one colour with the Color Mode of the job (Mean or Median of each channel). The channels are integers from 0 to 255.
- Generation copies these colours into the table and, for the intensity types, averages the channels as shown above. Intensity values can therefore have decimals.
- A well that has no measured colour on a photo (for example a well cut off
by cropping) gets
0in that photo's columns.
Higher values mean a lighter colour in that channel. The values are raw colours of the photo: differences in lighting between plate positions stay in the data. To correct them, use an adjustments table.