Exporting Data

Depending on the type of data that should be exported (scan data, tabular measurements, or single images/videos), OPTARI provides different export paths:

Full Scan Export (HDF5)

Exports the loaded scan together with any drawn ROIs and derived layers (new reconstructions, unmixed chromophore maps, SO₂/THb) into an HDF5 file that uses a custom, PATATO-inspired format carrying IPASC-conform metadata. This way, you can also convert proprietary vendor data (e.g. iThera .msot) into an open, shareable format by importing the scan into OPTARI and exporting it again. OPTARI cannot write back into the proprietary vendor format.

From the Scan Browser dock, click Export HDF5 and choose a destination.

ROIs from other tools (e.g. annotations made in the vendor software) are always written exactly as stored in the scan. If you edit one in OPTARI, the edited shape is saved as an OPTARI ROI next to the original, and removing one in OPTARI does not remove it from the export.

IPASC Export

Click Export IPASC to write the scan's raw time series as a native IPASC file. After a successful export OPTARI reports how many IPASC minimal metadata fields the file contains.

Warning

The IPASC format covers raw time series data only. Reconstructions, ultrasound, unmixed layers and ROIs are not included. Use the HDF5 export above to keep them.

Warning

Both HDF5 exports always write to a new file. OPTARI never changes the source file, and if a file with the same name already exists at the destination, the export fails.

Saved Analysis Table Import/Export (XLSX)

Click Export XLSX in the ROI dock to write the entire Saved Analysis table to a spreadsheet. The export always includes the full computed feature set, regardless of which columns are currently visible in the live view (see ROI Annotation). The exported tables can be used for further statistical analysis.

The file contains two sheets: roi_table with the measurements, and optari_meta with additional info (tool version, operator, analysis ID, creation time, schema version), mirroring the file_origin attribute written by the HDF5 export.

The filename is roi_data_<operator>_<analysis ID>_<timestamp>.xlsx, built from the OPERATOR and ANALYSIS_ID settings (see Configuration) with timestamp matching the creation_time in the metadata sheet.

The same file is written automatically as a backup after every change to the Saved Analysis table, one file per session: ~/.optari/autosave/roi_table_<date>T<time>_<pid>.xlsx, named after the session's start time and process ID (the matching log file in ~/.optari/logs/ has the same name). If OPTARI closes unexpectedly, start it again and import the newest backup from before the crash. The newest 20 backups are kept.

Using the Import XLSX button, you can load a previously exported analysis file back into the Saved Analysis table, allowing you to continue an earlier analysis or continue on a different machine. Import appends to the current table, so analyses from several sessions or machines can be combined in one place. roi_group_uid keeps every row attributable to the ROI it was measured from. Identical rows are skipped. Files written by a OPTARI version with an incompatible table schema are rejected.

ROI Analysis Plot Exports (PNG/...)

The Analysis Plots (histograms, spectra, time analysis) can be exported into PNG, CSV, or other image and data formats by right-clicking into the respective plot, choosing Export. The right-click menu also lets you configure the axes formatting and other plot options.

Tip

To set the size and aspect ratio of the exported image, undock the panel using the button on the top left of the plot, left of the Refresh button. This allows you to freely resize the plot before exporting it.

Viewer Export (PNG/TIFF/MP4)

Clicking the Export View button in the Scan Browser dock exports whatever is currently displayed in the viewer, using the current settings regarding visibility, overlay, colormap, etc.

Checking the Include colorbars box determines whether the colorbar should be displayed in the exported image. Views can be exported into .png or .tiff files.

Alternatively, the entire sequence of frames can be exported into a .mp4 video by checking the Video box. You can also provide the frame rate (FPS) for the exported video.

Tip

To set the size and aspect ratio of the exported image or video, resize the surrounding docks on the left, right and bottom of the viewer using the 3 dots on each panel. These will determine the borders of the exported image / video.

Tip

To set a specific, fixed contrast limit for the exported video instead of auto-scaling, see FAQ.