Using Stainfinder with TreeView

If you have correctly configured your web server and Stainfinder, and if you have a clustered data sets prepared, then you are ready to start using Stainfinder with TreeView.

1. Open the TreeView program and load your clustered dataset. If you have not already done so, proceed to the walkthrough for generating a clustered dataset of your TMA data. Alternatively, you may download the demo clustered datasets from the Downloads section and use that instead.
2. You may now click on one of the descriptors (shown below) to view the corresponding spot images from your collection.


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3. A new browser window will open, and you should get a screen like the one shown below (depending on how many antibodies stains you have available on your digital image collection for that particular core):


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Here, the default settings will be selected. The thumbnail images will be shown in the same browser window, and you can select a percentage value of the original image size for those thumbnails. You should also select the correct maximum resolution for your monitor, since Stainfinder will size the browser window of zoomed images (more on this in the next step). You will notice that Stainfinder will provide a list of all available antibodies for that particular core sample, with the relevant antibodies preselected, based on your data set being viewed in TreeView. You may alter your selections as desired. In addition, if you wish to retain your altered selections, choose your appropriate options, and a cookie will be set on your computer.

4. Click on "Display checked images". You should get a screen like the one shown below (depending on your selection of antibodies):

   
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   You will notice that the images retrieved correspond to either the antibodies present in your datasets, or your own selections. This is a helpful feature for comparing the scores shown in your dataset under TreeView with the actual stain images.

   Note: you may have to scroll down to see your images. In addition, if an antibody appears more than once in your data set (as shown earlier in this TreeView example), it will be displayed only once with Stainfinder.

5. You may now click on the link corresponding to one of the images. This will bring up the browser window containing the full-size image, allowing you to browse the image in full detail:


Click here for a larger view

You are now ready to use Stainfinder with TreeView to verify scores, compare stains, or perform any other function that would assist you in exploration of your digital image collection and corresponding data analysis.

You may also explore an on-line version by clicking here.

Back to Step 2.