Tissue Microarray De-Arraying Tool

Uploading an Image

Start by uploading an .svs, .tif/.tiff, or .ndpi image for optimal results. While you can use .png or .jpg files, please note that virtual gridding functionality may be limited with these formats.

Once the image has been successfully uploaded, click the Proceed button to continue to image segmentation.

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Dimensions --

Export Load an image to check support

Demo image HE Hamamatsu tissue microarray

Completing Core Segmentation

Adjust segmentation parameters in the left-hand menu to optimize core detection. If necessary, make manual edits to ensure all cores are accurately captured.

Once you're satisfied with the segmentation, click the Proceed button to proceed to the Gridding tab.

Interactive Core Editing

Click on the image to add a core.

Shift-click a core to remove it.

Segmentation Parameters

Preset Mask Alpha: 0.2 Sensitivity: 0.05 Min Area: Max Area:

Advanced segmentation

Distance Transform Multiplier:

Parameters are current.

Detected: -- Rescued: -- Removed artifacts: -- Recentered: --

Gridding Instructions

Open the menu on the left to adjust the gridding settings and key hyperparameters such as as the image's rotation. Please ensure that the image is rotated correctly. If not, adjust the image rotation parameter.

Once you're satisfied with the gridding, click the Proceed button to proceed to the Virtual Grid section.

Marker cores are now placed automatically when the surrounding row and column lattice can be inferred confidently.

Editing Cores

You can move the core by dragging it to the desired location.

Click the core, then drag the corner anchor points to resize.

Double-click the core to open the edit menu and change its metadata.

Shift-click the core to toggle its status as real/imaginary.

Adding Cores

Click the Add Core button in the top left corner, then drag to set the core's location and size.

Marker core placement will be checked after gridding runs.

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Configure Parameters

Image Parameters

Core Radius: 20

Traveling Algorithm Parameters

Image Rotation: 0

Display Parameters

Connect Cores

Flag Misaligned Cores

Advanced Settings

Traveling Algorithm Parameters Radius Multiplier Grid Width Stopping Distance Multiplier for Grid Width Image Width Search Angle

Edge Detection Parameters Length Threshold Multiplier Threshold Angle

Image Rotation Parameters Minimum Angle Maximum Angle Angle Step Size Angle Threshold

Is a Marker

Row: Column: X Position: Y Position: Radius: Annotations:

Normal Missing

Core Color Legend

Marker cores.

Normal cores.

Misaligned cores.

Imaginary cores.

Utilizing the virtual grid

Select a core in the right-hand grid to edit its metadata. Remember to click Update Metadata to save your changes.

Click the Add Field button to add a column to your associated metadata file.

To export a single core at full resolution, Double-click it. To export all cores, click the Export Grid button. Note that core exporting is only enabled for .svs files

Edit Metadata

Export Progress

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