To get started, you have to copy your svs files (e.g. the example data from the openslide project) to the folder "incoming_svs_files". Then, access the web application, e.g. at: http://localhost/cip2/website/index.php

There, click on "Process Incoming Folder". You should see now a list of files in "incoming_svs_files". Start tiling by pressing the button. Tiled versions of the svs images should now be generated in the folder "virtualmicroscope". When tiling was performed correctly, on the main page you should see now entries of the images with thumbnail pictures. Click on one of it to start the viewer.

00Specimens_list

In the viewer, you can define a region by clicking somewhere in the image. A marker will be put at the position. You can remove a region by clicking on the marker again, and choose "remove" in the menu that pops up.

01removeMarker


After having defined some regions, you can click on "Compute ATh" to apply an adaptive threshold algorithm to that regions.

02computeAth

You should see a list of the coordinates of all the regions that will be used. The results will be saved in virtualmicroscope//work_collections/test_collection

03usedRegions

If you enter again in the same way to the page but computation has not finished yet, you get a progress bar:

04iP


In the subdirectory "regions", there are the exported regions and the results from the filter. In "filter_results", there are the tiled versions of the filter results. You can now use the "Filter results..." menu in the viewer (right upper corner) to enable and disable the overlay of the filter results onto the original image.

 

06fR2


Currently, only the adaptive thresholding is included in the GUI. However, a bunch of other algorithms is included. These have to be applied manually to the images, and later you can import any filter result using "Import Collection".