Digital histology

When opening the Pannoramic Viewer you see all of your virtual slides in thumbnail view. Selecting one (or up to 10 at a time) the slide gets under the virtual objective of the virtual microscope. Here you can move and change the magnification of the slide quickly and easily using the mouse. Emphasizing 'quickly' is important considering the fact that the size of an average virtual slide can easily be more than 1 GB.

Main characteristics:

• Seamless zooming and moving of the virtual slide
• Bookmarking (annotating) on the spot, i.e. defining the specific part of the sample by drawing; finding and reading of previously made bookmarks
• Easy and precise measurements
• Real-time changing of brightness, contrast and color bias
• Fluorescent slide handling, separate channel view & pseudo-colorization
• Slide uploading and downloading for teleconsultation
• Synchronized viewing (moving and zooming) of multiple slides for comparison purposes
• Publication quality image capture of displayed areas (.JPG, .BMP, .TIFF)
• TIFF, MIRAX slide and Meta-XML export for Carl Zeiss AxioVision™ compatibility
• Scanmap export for rescanning existing digital slides
• Easily expandable functionality via the software modules

NuclearQuant is a QuantCenter module. It is designed for cell nuclei detection and quantification of IHC stained samples. NuclearQuant measures several morphological features besides stain intensity. The cell nuclei classification and the final score are calculated by the intensity score and the proportion score.

DensitoQuant is a simple and fast, yet effective tool for IHC measurements. It measures the density of immunostain on the digital slides by distributing pixels to negative and 3 grades of positive classes by their RGB values. DensitoQuant is especially suitable for quick TMA evaluation. Analyzing a whole digital slide takes only a couple of minutes.

This plugin is bundled with Fiji. For installation in ImageJ1, download from the link below and manually install the class file. 

Quote:

The colour deconvolution plugin (java and class files) for ImageJ and Fiji implements stain separation using Ruifrok and Johnston's method described in [1]. The code is based on a NIH Image macro kindly provided by A.C. Ruifrok.
The plugin assumes images generated by colour subtraction (i.e. light-absorbing dyes such as those used in bright field histology or ink on printed paper). However, the dyes should not be neutral grey (most histological stains are not so).
If you intend to work with this plugin, it is important to read the original paper to understand how new vectors are determined and how the procedure works.
The plugin works correctly when the background is neutral (white to grey), so background subtraction with colour correction must be applied to the images before processing.
The plugin provides a number of "built in" stain vectors some of which were determined experimentally in our lab (marked in the source with GL), but you should determine your own vectors to achieve an accurate stain separation, depending on the stains and methods you use. See the note below.
The built-in vectors are :

• Haematoxylin and Eosin (H&E) x2
• Haematoxylin and DAB (H DAB)
• Feulgen Light Green
• Giemsa
• Fast Red, Fast Blue and DAB
• Methyl green and DAB
• Haematoxylin, Eosin and DAB (H&E DAB)
• Haematoxylin and AEC (H AEC)
• Azan-Mallory
• Masson Trichrome
• Alcian blue & Haematoxylin
• Haematoxylin and Periodic Acid - Schiff (PAS)
• RGB subtractive
• CMY subtractive
• User values entered by hand
• Values interactively determined from rectangular ROIs