Slide Analysis

Examine, organize, and annotate slide images.

Start Microscope Slide Analysis

On this page, select the slide Acquisition(s) that you want to examine, organize, and annotate.

  1. Click Image Gallery.

  2. In the Select Acquisition dialog, use CTRL + Click (Command + Click on macOS) or SHIFT + Click to select multiple Acquisitions.

    Empiria Studio slides multiple acquisitions selected
    Multiple selected slide Acquisitions.
  3. Click Select.


To help with record keeping, give every Experiment a distinct name. The description field provides space for you to include important details about the Experiment.

Set up images

On the Set up images page, add images from your chosen Acquisitions to the figure. On the Report page, you can export this figure as a single image file.

  • Add the images in the order you want them to appear in the figure. Rows are created automatically as you add images.

  • Click Adjust All Display to simultaneously adjust the display settings for all the images and to make the display settings the same for all the images. Move the Adjust All Display Controls dialog to the side of the Empiria Studio window to watch how the images change as you change the display settings.

  • Right click an image, and then click Remove Image... to remove an image from the grid.

Empiria Studio slides set up images

Annotate Image

Click the zoom buttons above the image to make the displayed image smaller or larger . A zoom level, shown as a percentage relative to the size of the software window, is shown next to the zoom buttons. When the image is zoomed in, click and drag the image to see a different part of the image.

Shapes, text, and a scale bar can be added on this page. When an annotation is added, options specific to that annotation are displayed in the Options section of the control pane. The scale bar or text box can quickly be moved to one of the corners of the image by clicking a corner option Empiria Studio place object in top right corner icon Empiria Studio place object in bottom right corner icon Empiria Studio place object in bottom left corner icon Empiria Studio place object in top left corner icon in the Options section.

Click Empiria Studio brightness and contrast gear icon to adjust the display settings for images individually.

To delete a selected annotation, click Delete or press Delete on the keyboard.


On the Review page, you can see review how the figure looks in its entirety. Navigate to one of the previous pages to make changes.

You can also add a figure legend if you'd like. The figure legend will be part of the exported figure image.


Expand Sections

The data in the report is organized into sections. Click to expand a section to view data and export options.


Scroll to the bottom of the page to find the Summary field. Be sure to record your observations and conclusions in the Summary field for future reference.

Export images

  • If you want to view your slide images in a third-party software (e.g. Fiji), select the slide Acquisition in the Image Gallery and click Export to Analyze. Locate the exported Zip File and extract it. Use the TIFF file in the extracted folder in the third-party software. Do not attempt to analyze files exported for publication or presentation.

  • Click Export above an image to export the image. Images can be exported as a high resolution TIFF for publication in a journal or as a PNG appropriate for slide show presentations. Do not use these images for analysis.

  • The units for image size can be set to English or metric on the General Options page.

  • Click Hide features to hide annotations. If annotations are hidden, they will not be included in the exported image or report.

Export PDF Report

Click PDF Report to export a PDF of the images and data on the Review and report page.


Rate the Experiment for you records. This is an opportunity to record if the Experiment went "well" or not, depending on the specific requirements for your research.

Your rating will appear in the Experiment list for the Project.


Click Done to mark this Experiment as complete and return to the Experiment List.