Date Published: July 6, 2017
Publisher: Public Library of Science
Author(s): Vincenzo Della Mea, Giulia L. Baroni, David Pilutti, Carla Di Loreto, Helmut Ahammer.
The digital slide, or Whole Slide Image, is a digital image, acquired with specific scanners, that represents a complete tissue sample or cytological specimen at microscopic level. While Whole Slide image analysis is recognized among the most interesting opportunities, the typical size of such images—up to Gpixels- can be very demanding in terms of memory requirements. Thus, while algorithms and tools for processing and analysis of single microscopic field images are available, Whole Slide images size makes the direct use of such tools prohibitive or impossible. In this work a plugin for ImageJ, named SlideJ, is proposed with the objective to seamlessly extend the application of image analysis algorithms implemented in ImageJ for single microscopic field images to a whole digital slide analysis. The plugin has been complemented by examples of macro in the ImageJ scripting language to demonstrate its use in concrete situations.
The digitalization of full glass slides containing tissue samples for microscopic analysis is a reality that is becoming stronger and opens to many opportunities . The digital slide, or Whole Slide Image, is a digital image, acquired with specific scanners, that represents a complete tissue sample or cytological specimen at microscopic level. Having such samples in digital form brings many advantages such as the immutability of the sample along time as well as the possibility to analyze it more automatically using many different image analysis methods. However, digital slides are acquired at resolutions up to 0.2 μ/pixel, thus consisting of up to billions of pixels. Image size is one of the reasons why they are not yet commonly used in routine.
Whole slide images cannot always be directly opened and processed with ImageJ and similar software, due to the need of being fully loaded in main memory, which is not often practically possible.