Projects and Tables

Slide Set projects organize data into tables. Each table column specifies one field in the dataset, and each row specifies the individual values of those fields for one entry in the set.

Any table can be used as input data for a Slide Set analysis command or plugin. Table columns are matched to command inputs, and the analysis is repeated for each table row. Analysis results are stored in a new table linked to the input data table.

Example Slide Set data table containing images, regions of interest, and group identifiers.
Image ROI Group
img1.tif roi/roi1.roiset "Control"
img2.tif roi/roi2.roiset "Control"
img3.tif roi/roi3.roiset "Control"
img4.tif roi/roi4.roiset "Treatment A"
... ... ...

Project files

Use the File menu to create, save, and open project files. The directory where a project file is saved will determine the default storage location for linked resources such as ROI sets. New projects contain a single base data table. Results from commands run on the base table will produce additional tables within the project.

Project information and all table data are stored using an XML format. Data from individual tables can be exported as comma-separated spreadsheets by selecting Table > Export Data As CSV.

Editing tables

To edit a data table, double-click on the table in the Slide Set launcher or select Table > View Table from the menu.

Columns and rows can be added to or removed from the table using the Column and Row menus. Each column must have a specified data type, which defines what information it can store and which command input variables it can fill. The available data types are listed below.

Data elements can be entered individually, or multiple elements (of the same type) can be set together by selecting them, right-clicking, and choosing Set Selected Values from the popup menu. Data elements that contain file names, such as images or ROI sets, can be set by dragging the image file onto a cell (to change an existing value) or column header (to add the link in a new row).

To save table data, choose File > Save from the Slide Set launcher menu. To export individual tables, choose Table > Export Data As CSV.

Data types

Four basic data types are available, all of which are stored directly in the data table:

  • Logical (true or false)
  • Integer
  • Numeric
  • Text

Other data types can be stored in separate files, with the file names listed in the table. Possible file types include image files (any format recognized by ImageJ), regions of interest, and other file formats specified by MIME type.