Batch analysis

Part of Dioptra Lab. Importing a single file, plate-reader exports included, and replacing a table’s data are free.

A template is any project plus the table that receives the data. Batch analysis puts each data file into a copy of the template, recomputes every formula, analysis, graph and layout, and writes:

• <file>.dioptra, the recomputed project;
• <file> - <graph>.pdf (or .png, .svg) for every graph and layout, at its set size;
• summary.csv, one row per file.

Files are read as by Replace table data: names and column formulas of the receiving table stay, the data change. A plate map, if given, applies to every plate-reader file.

The summary

The summary has a File column, one column per headline number and an Error column. Headline numbers come from every section of every results sheet: the columns headed Value, Best-fit or Estimate, and every column of p values. Each is named after the analysis and the row, such as Fit · Data set A · LogEC50. A nonlinear fit gives its parameters (Bottom, Top, LogEC50, HillSlope) and derived values (EC50); a t test gives t, df, the P value, the difference and the effect sizes. Rename an analysis in the template to name its columns.

A file that cannot be analysed (no data, a table of the wrong kind) gets its error in the summary; the others go on.

In the app

File → Batch analysis… asks for:

• the template: the open project, or a project file;
• the table that receives the data;
• the data files (on the desktop, files or a whole folder);
• the figure format and an optional plate map;
• the output folder (desktop). In the browser, everything downloads as one zip.

The dialog shows progress and, at the end, the summary and any errors.

File → Watch a folder… (desktop) applies a template to each new file that appears in a folder, once its size has stopped changing for two seconds. Results go to the folder’s analysed subfolder, with a summary.csv that grows by one row per file. Files already in the folder are left alone. File → Stop watching the folder ends it; so does quitting.

From the command line

dioptra batch assay.dioptra --table "Plate" exports/ --out results --format png

Inputs are files or folders (their data files, not subfolders). --plate-map map.txt applies a plate map; --dpi sets the PNG resolution (300). The exit status is non-zero when any file fails.

The key is read from $DIOPTRA_LICENSE, or from the file the desktop app keeps:

dioptra license shows it, dioptra license --set <key> stores it and dioptra license --remove deletes it.