Description

Controls data export for each analysis run (job) as well as providing the option to run a final macro on all data. If running a single file analysis, by default, the spreadsheet will be saved with the same name as the input file and stored at the same location. Whereas, in batch mode (running multiple files from a folder) the spreadsheet will be saved in that folder with the same name as the input folder. Using the "Group save location" parameter it's possible to redirect the output spreadsheet(s) to a specific location.

Data can be collated into a single Excel spreadsheet, or exported as one spreadsheet per analysis run (job). Exported spreadsheets are separated into multiple sheets:

It's also possible to select the data to be exported for each sheet, including the metadata values (filename, series number, etc.), individual measurements and object collection statistics.

Parameters

Add variable (default = "") Pre-define variables, which will be immediately accessible within the macro. These can be used to provide user-controllable values to file-based macros or to prevent the need for editing macro code via the "Output control" panel.
Variable type (default = "Text")
Variable name (default = "") The variable value can be accessed from within the macro by using this variable name.

Variable checkbox (default = "true")

Variable numeric value (default = "0.0")

Variable text value (default = "") Text value assigned to this variable.


Run macro (default = "false") When selected, a final macro can be run once all the analysis runs (jobs) have been completed. By using the workspace handling macros ("MIA_GetListOfWorkspaceIDs" and "MIA_SetActiveWorkspace") it's possible to switch between workspaces, thus facilitating dataset-wide analyses. This macro will be executed only once as part of the final data exporting phase of the analysis.

Macro mode (default = "Macro text") Select the source for the macro code:

Macro text (default = "run("Enable MIA Extensions"); // Get a list of Workspace IDs with Ext.MIA_GetListOfWorkspaceIDs() and set active workspace with Ext.MIA_SetActiveWorkspace(ID).") Macro code to be executed. MIA macro commands are enabled using the "run("Enable MIA Extensions");" command which is included by default. This should always be the first line of a macro if these commands are needed.

Macro file (default = "") Select a macro file (.ijm) to run once, after all analysis runs have completed.

Export mode (default = "All together") Controls the number of results spreadsheets that are exported and what they contain:

Individual save location (default = "Save with input file") If "Export mode" is set to "Individual files" this parameter controls where the individual results files are saved:

Group save location (default = "Save with input file") If "Export mode" is set to "Group by metadata" this parameter controls where the grouped (by metadata) results files are saved:

File path (default = "") The path to the folder where results will be saved if using a specific folder path.

Mirrored directory root (default = "") If using a mirrored directory structure for the results files, this parameter specifies the output structure root. Subfolders will be created within this root folder that have identical structure to the subfolders of the input folder.

Save name mode (default = "Match input file/folder name") Controls how the output results filename is generated:

File name (default = "") Name to save the results file with if saving results files with a specific name ("Save name mode" parameter).

Metadata item for grouping (default = "") If "Export mode" is set to "Group by metadata", results will be grouped and saved by the value of this metadata item associated with each analysis run. There will be one results spreadsheet for each unique value of this metadata item.

Continuous data export (default = "false") When selected, the results spreadsheet(s) can be exported at intervals during a multi-analysis run. They will be exported every N runs, where N is controlled by the "Save every n files" parameter. The spreadsheet(s) will still be stored when all analysis runs have completed.

Save every n files (default = "10") If "Continuous data export" is enabled, the current version of the spreadsheet will be exported after every N analysis runs. This means if the analysis fails or the computer crashes, results collected so far are not lost.

Append date/time mode (default = "Never") Controls under what conditions the time and date will be appended on to the end of the results file filename. This can be used to prevent accidental over-writing of results files from previous runs:

Export summary (default = "true") When selected, a summary sheet will be added to the results spreadsheet. The summary sheet contains either (1) one row per input image file, (2) one row per timepoint per image file or (3) one row per metadata item. The export mode is controlled by the "Summary mode" parameter. This sheet is given the name "SUMMARY" and contains statistics for measurements (mean, min, max, standard deviation and sum), object counts and metadata items.

Summary mode (default = "Per input file") Controls the form of the summary sheet (if "Export summary" is selected):

Metadata item for summary (default = "") The metadata item to group the rows of the summary sheet by if "Summary mode" is set to "Group by metadata".

Show object counts (default = "true") When selected, the "Summary" results sheet displays columns reporting the number of objects per object collection.

Export individual objects (default = "true") When selected, individual results sheets will be created for each object collection. In these sheets, each object in that collection is summarised per row. The individual object sheets have names in the format "OBJ_[NAME]", where "[NAME]" is the name of that object collection.