The summary report is meant to sum up the most important findings in a compressed manner in a file, which can be exported to be opened outside of Aivia. For this, a selection dialog can be used to select the items to be added to the report, the file type must be chosen, and the report will be created.

General usage

The summary report export can be started by going to File > Export > Summary Report or by pressing the hotkeys Ctrl + Shift + R. This will open the “Summary Report Item Selection”-dialog (see image right).

Item Selection

All items that should be added to the report must be created and present in Aivia when starting the report process - the “Summary Report Item Selection”-dialog will display items, depending on the current state in the Aivia software - except for charts which have to be added to the report from within the “Charts”-panel (detailed description below).

In the “Summary Report Item Selection”-dialog, you can select the desired elements to be exported by clicking on the checkboxes next to them and/or by using the Select All Items button on top.

On each summary report, the date, time, and Aivia version is added.

Image will add a copy of the image, at the current zoom level if fitting onto a page, otherwise, it will be shrunk accordingly. Additionally, information about the name of the image, the folder it is saved in, the image dimensions and calibration are added.

Channels will add a table of all channels of the current image, with information about the channel name, color and the origin.

Channel Groups will add the list of all channel groups and their content.

All Object Sets will add all object sets/subsets, independent of their type in a table, including names, object counts and percentages for subsets, and information how they were created (origin) if available.

Underneath is a list of all types of object sets (Cells, Neurons, Outlines, Meshes, Tracks, Whole Image) to select them individually.

All Object Subsets will add all object subsets, independent of their type.

Underneath is a list of all types of object subsets (Classes, Phenotypes, Gating) to select them individually.

Set Creation Info will add information about how the object sets/subsets were created (i.e. recipe or classifier parameters).

Region of Interest will add a table with information about the regions of interest, including their name, area, and type.

Charts will add all charts that were previously added to the report from within the charts panel.

Underneath is a list of all chart types (Summary View, Histogram, Scatter Plot, Binned Scatter Plot, Trace Plot, Directional Plot, Lineage Plot, Flow Plot, Kymograph, Violin Plot, Pearson Heatmap, Dendrogram, Dim. Reduction) to select them individually.

Saving the report

After selecting all desired items, clicking the “Save”-button will open a “Save Report”-dialog to choose the save location and the file type (Markdown, HTML, Word document). Clicking “Save” in the “Save Report”-dialog will save the report in the chosen location. Together with the report itself, a subfolder will be created which contains all images, that will be displayed in the report.

Viewing the report

Markdown: This option will create a file in markdown format (.md, Markdown - Wikipedia). To view the markdown file in a human-readable form, it must be converted. There are multiple programs available for this (i.e. Visual Studio Code), including freeware.

HTML: This option will create a file in html format (.html, HTML - Wikipedia). To view the html file in a human-readable form, it must be opened with a designated program (i.e. a web browser).

Word document: This option will create a Word document (.docx). To view the Word document, it must be opened with a designated program (i.e. Microsoft Word).