Output control
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:
- "Parameters" An overview of the analysis setup (path to workflow file, date run, computer operating system) along with a list of all modules and parameters, their values and states. The information here should be sufficient to reconstruct the analysis workflow in the absence of the original workflow file.
- "Log" A list of any error messages presented to the user while the analysis was running.
- "Summary" Each analysis run is summarised by a single line (or one line per timepoint or metadata value, if selected) containing metadata values, image measurements, the number of objects detected as well as statistics for object collections (e.g. mean of a particular measurement). The summary sheet is intended to facilitate quick analysis; all data contained in this sheet (with the exception of image measurements) can be manually compiled from the individual object sheets. This sheet can be enabled/disabled using the "Export summary" parameter.
- "[Object-specific sheets]" Each object collection can export to a separate sheet. These sheets contain one row per object in that collection and include metadata values, along with all measurements and relationships for that object. This sheet can be enabled/disabled using the "Export individual objects" parameter.
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") Controls the data type of the variable that will be assigned within the macro:
- "Boolean" Variable will be assigned a true/false value depending on whether the checkbox was selected/deselected (respectively).
."Number" Variable will be assigned a numeric value to which mathematical operations can be applied.."Text" Variable will be assigned a text value. Irrespective of whether the value contains only numeric characters this will be interpreted as text.
- "Macro file" Load the macro from the file specified by the "Macro file" parameter.
- "Macro text" Macro code is written directly into the "Macro text" box.
- "All together" Results from all current analysis runs are grouped into a single spreadsheet. The same sheets are used for all runs, so it's necessary to include a filename (and where necessary, a series name/number) metadata identifier. Unless "Save name mode" is set to "Specific name", this file is named after the input file/folder.
- "Group by metadata" Results are grouped and exported by a specific metadata item associated with each analysis run. Unless "Save name mode" is set to "Specific name", the files are named in the format "[input file/folder name]_[metadata name]-[metadata value]". The metadata item to group on is specified by the "Metadata item for grouping" parameter.
- "Individual files" A separate results spreadsheet is saved for each analysis run.
- "None" No results spreadsheets are exported.
- "Mirrored directory" The files are saved in a mirrored directory structure. This structure has the same folder layout as all subfolders of the specified input folder. The root location of the mirrored structure is specified by the "Mirrored directory root" parameter.
- "Save with input file" The files are saved in the same folder as the input file. If a folder was selected as the input, the result files are saved directly inside that folder.
- "Specific location" The files are all saved in a single folder specified by the "File path" parameter.
- "Save with input file" The files are saved in the same folder as the input file. If a folder was selected as the input, the result files are saved directly inside that folder.
- "Specific location" The files are all saved in a single folder specified by the "File path" parameter.
- "Match input file/folder name" Results files are stored with the same name as the input file/folder (depending on the "Export mode" parameter).
- "Specific name" Results files are stored with a specific name, specified by "File name".
- "Always" Always append the time and date on to the end of the filename.
- "If file exists" Only append the time and date if the results file already exists.
- "Never" Never append time and date (unless the file is open and unwritable).
- "Per timepoint per input file" Each timepoint of each input image file is summarised in a separate row.
- "Group by metadata" All files matching a specific metadata value are averaged and summarised in a separate row (i.e. one row per unique metadata item).
- "Per input file" Each input image file is summarised in a separate row.