Vala Sciences

Once the initial analysis is complete, the image processing results should be inspected in the CyteSeer Image Viewer.

Open the viewer by selecting Images… from the View menu of the CyteSeer ViewRNA main window.

This will open a window allowing you to change the Image Naming Convention, Image Folders, Well Definition and Well Name to be viewed. The defaults are taken from the main CyteSeer window.

Highlight a well and click Ok to view the images for that well.

A window similar to that shown above should now be viewable. These are the original unprocessed images for the selected well. Resize and position the window as needed.

The simple interface allows access to a broad set of image viewing features.

Click the Set Images… button to open the initial image viewer settings window. This window can remain open as you select new wells for viewing. Large images may load slowly.

Click the Set Colors... button to open the Colors dialog. This is one of the more powerful tools in CyteSeer ViewRNA.

The Colors dialog controls what is seen in the main Image Viewer window through an array of checkboxes. All the images are updated as the relevant box is checked and can be kept open while working the images. This combination is a very powerful means to iteratively compare unprocessed images with their processed counterparts. It is an excellent way to view how well the image segmentation performs.

The upper section of the dialog controls how unprocessed images are displayed. If Show is checked for a given channel, raw image data will be visible. If Contrast is checked the unprocessed image’s contrast is stretched to better match the monitor for viewing. The original image data is unchanged.

The interior checkbox displays the entire mask region as a saturated color. The raw image data is completely obscured behind the mask. The example above shows the mask for two nuclei that look like they are fused together and the edge of a third.

The edge checkbox displays just the edges of the mask. Notice in the example how, it appeared that CyteSeer incorrectly fused the nuclei together into a single mask. Since there is a complete edge line shown breaking the nuclei into two, the edge mask shows that the nuclei were counted correctly.

The color can be selected on a channel by channel basis from a drop down menu in the dialog. The image, mask, bounding box, cell ID and crosshairs share the chosen color. Each channel can also have it's own color.

Cell ID. Each cell is given a unique ID number viewable via the appropriate checkbox in the Colors dialog.
Bounding Box. The bounding box for each sub-cellular region for a given cell is viewable via the appropriate checkbox in the Colors dialog.
Crosshairs. Crosshairs indicating the location of the centroid of each sub-cellular region for a given cell is viewable via the appropriate checkbox in the Colors dialog.

The image zoom can be adjusted via the zoom drop down menu. Increasing zoom is useful to view smaller sub-cellular regions and to closely inspect the performance of an image processing algorithm. Decreasing zoom is useful for getting an overview of images larger than the computer monitor in use. Increasing the zoom will increase the required memory for CyteSeer ViewRNA. Using large images with a high zoom can potentially crash the program if your system runs out of available memory.

Save the Image. Click the Save Jpeg button to save the current active view in the Image Viewer at any time. Please add the .jpg extension to any filename you choose.

Use the Image Viewer for detailed visual analysis of image processing results. The next section of the tutorial describes how to best iteratively adjust the settings of the main window until the appropriate processing results are achieved.