How do I export results?

How do I export results?#

What will I learn?

  1. How to export results from a single image.

  2. How to export results from all images in a project.

Viewing measurements (again)#

After you’ve analyzed images with QuPath, you may want to export the results for analysis in suitable software.

In “How do I count cells?”, we saw how to access the measurement tables for the various object types in the current image via ../../_images/TABLE.png button. This allowed us to view a table of annotation measurements or detection measurements.

QuPath makes it easy to copy and paste this table into other software.

What to do

  1. Select Measure ‣ Show annotation measurements.

../../_images/annotation_table.png

Fig. 74 The annotation measurement table#

  1. Select some annotations using Control/Command or Shift

  2. Copy the data to the system clipboard by clicking Copy or pressing Control/Command+C.

  3. Paste the data into a text editor or spreadsheet program of your choice.

../../_images/annotations_excel.png

Fig. 75 Annotation measurements opened in a spreadsheet program#

If you would prefer to export all annotations then you can select all entries in the table using Command/Control+A. To re-order the annotations based on a specific value, you can click on a column.

Exporting measurements from multiple images#

Returning to OS-2.ndpi, let’s try to export measurements from multiple images. To do this, QuPath includes a more comprehensive exporting tool.

But first, we need multiple images! For convenience, we’ll just duplicate the current one.

What to do

  1. Open OS-2.ndpi.

  2. Select Duplicate image.

  3. Keep the Also duplicate data files checkbox selected.

  4. Click OK.

Now, let’s get exporting.

What to do

  1. Open Measure ‣ Export Measurements…

  2. In the resulting dialog, select one or multiple images within Available and click > to move images across into the Selected list.

../../_images/export_measurements.png

Fig. 76 Export measurement window#

Alternatively, if all of the images are of interest then select >>. 7. Complete the remaining fields:

  • Output file: Determine where your file is going and what its going to be called.

  • Export type: Choose which objects you want to export.
    Here, we’ll select Detections.

  • Separator: Controls the value separator, i.e., controls whether the output is csv or tsv.

  • Columns to include: Define which measurements you want to export. Here we will be selecting them all. If you are choosing specific measurements, click Populate after selecting Export type. This may take a few seconds.

    ../../_images/export_measurements_complete.png

    Fig. 77 Export measurement window#

    You can now choose a subset of the available measurements, rather than exporting everything.

  1. Click Export.

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