Introduction

Numeric results generated by MIA workflows are exported to Excel spreadsheets. By default, each time a workflow is run, the results for all images processed will be collected into a single spreadsheet, however, this behaviour can be changed such that each input file generates its own spreadsheet.

Output results files can contain multiple, highly configurable sheets. Typically, a results file will include a summary sheet with one row per input image, individual object sheets with one row per detected object and a couple of record-keeping sheets.

The output file format is configured in the "Output control" module.

Summary sheet

The summary sheet is intended to provide a quick overview of the measurements contained within the individual object sheets. Information is broken down into four classes of column.
- By default, each row of the summary sheet will summarise the results from a single input image.
- By changing the "Summary mode" parameter of the "Output control" module to "Per timepoint per input file", a new row can be generated for each timepoint in the image, allowing for quick analysis of time-dependent processes.
- Alternatively, by setting this to "Group by metadata", results can be grouped by a specific metadata item, with one row per unique metadata value.
Metadata values:
- Record input file-specified properties, such as filenames and series numbers.
- These are important for result filtering and sorting, since results from multiple files may be included in a single results file.
- Column headings simply state the name of the metadata item.
- Metadata columns can be enabled/disabled using the "Ind" controls in the "Output control" module.
Image measurements:
- These columns record the individual measurements assigned to each object.
- Columns headings are in the form:
- For example, an image called "Binary" with the measurement "THRESHOLD // GLOBAL Huang" would be called "Binary_(IM) // THRESHOLD // GLOBAL Huang".
- Image measurements columns can be enabled/disabled using the "Ind" controls in the "Output control" module.
Object counts:
- These simply state the number of objects of the specified class.
- These have headers in the form:
- For example, for the count of detected "Nuclei" objects, this would be "Nuclei_(OBJ) // NUMBER".
- Object count columns can be enabled/disabled using the "Show object counts" control in the "Output control" module. Object counts are either on or off for all objects.
Object measurement statistics:
- Since multiple objects may be detected for an input file, each with their own measurements, these columns provide a single summary measurement statistic.
- Headers for these values are in the form:
- For example, the header corresponding to the mean of the "SHAPE // N_VOXELS" measurement for "Nuclei" objects would be "Nuclei_(OBJ_MEAN) // SHAPE // N_VOXELS".
- Supported statistics are the mean ("MEAN"), minimum ("MIN"), maximum ("MAX"), standard deviation ("STD") and sum ("SUM").
- Object measurement statistic columns can be enabled/disabled using the "Mean", "Min", "Max", "Sum" and "Std" controls in the "Output control" module. The "Ind" control determines if the measurement appears in the object-specific results sheet.

Object sheets

The individual object sheets include the individual measurements for each detected object. Each row of an object results sheet corresponds to a single detected object.
The first column is always ("OBJECT_ID"), which is the unique ID number for that object in that analysis run.
- Note: IDs are only unique to that analysis run, so if multiple input files were processed, the same ID numbers will likely appear.
As with the summary sheet, each row has columns for file-specific metadata items as well as a column for each exported measurement.
Metadata and measurement columns can be disabled with the "Ind" controls in the "Output control" module.

Record-keeping sheets

The final two sheets are always record-keeping sheets. These are useful for retaining knowledge of how a workflow was run (e.g. plugin version) as well as seeing if any errors occurred during execution.
The "Configuration" sheet includes some device-specific information such as the computer operating system, plugin version and date/time of execution. It also includes a full copy of the .mia workflow file used. In the event of the workflow file being lost, these rows can be copied into a text file and saved with the .mia extension.
The "Log" sheet contains a list of any error messages encountered during the analysis run. All being well, this sheet should be empty.

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