Overview

Tissue microarrays (TMAs) are commonly used to analyze multiple tissue cores on a single slide. The Enable Cloud Platform supports upload of whole-slide TMA images and downstream analysis of TMA cores. This document provides guidance on how to import and work with TMA data on the Enable Portal. These steps can also be followed to import any whole-slide image containing multiple tissues.

Upload images

1. When creating your experiment through the Upload Data workflow, indicate that you have one sample per image file. The number of samples/cores in your TMA will be automatically updated in later steps.

Split images into individual cores

1. Once images are available on the Visualizer, open the Image Splitter Panel.
2. Follow instructions given in Image Splitter Panel to either draw or auto-detect the boundaries of each core in your TMA.
3. Kick off the splitter by clicking Run Image Split.

Label samples and upload metadata

1. Once your split images are available to view in the Visualizer, you will be able to update sample labels.

2. View your new experiment. It should now have N samples and N regions, where N corresponds to the number of boxes that were drawn in the Image Splitter. The sample and regions have a 1:1 mapping.

3. Go to the Label Samples tab. To the left, you will see an overview of the original TMA image with a dot overlaid at the center of each core. Each dot is labeled with a number (between 1 and N), which corresponds to the default sample label that is listed on the right (screenshot below). Currently, the default sample label for each region is “Split Sample [N]”.

   

4. To update a sample, click the edit button (pencil icon) to the right of a sample label. The following view will appear. You can then change theSample Label field and click Update.

   

   After clicking the edit button for “Split Sample 1”.

5. If multiple cores belong to the same sample (i.e. they are sourced from the same piece of tissue), you can associate them to the same one using the following steps. As an example, the steps to associate the first two cores (”Split Sample 1” and “Split Sample 2”) to the same sample (named “Patient A - Normal”) will be shown.

   1. First, edit one of the samples, remove the associated Regions (so that the Regions field is empty), and click Update. The label will be updated to say “No sample specified”.

      

      Edit “Split Sample 2”. Empty the Regions field. Then click Update.

      

      “Split Sample 2” is updated to “No sample specified”.

   2. Next, edit the other sample and add the region that was just disassociated to this sample to the Regions field. Available (unassociated) regions will appear in the dropdown menu. At this time, you may also choose to update the Sample Label from the default label to something more meaningful. Click Update when you are finished.

      1. test

      

      Edit “Split Sample 1”. Click the Regions field.

      

      Add the second region to the Regions field. Update Sample Label to “Patient A - Normal”. Then click Update.

      

      “Split Sample 1” and “No sample specified” are both updated to “Patient A - Normal”. Click Save to finalize updates.

   3. Repeat these steps for as many region sets as needed.

   4. Click Save when finished with all changes.

6. When uploading sample/clinical metadata, make sure that the sample labels designated in the Sample Labeler match those in the uploaded CSV.