2D

The skin tools measure the thickness of the epidermis and the interdigitation index.

The input images are masks that represent the epidermis and that have been created from images of stained histological sections. The mask must touch the left and right border of the image. The dermal-epidermal border must be on the lower site of the image. The interdigitation index can be measured for one or more segments per image. As a measure of the thickness of the epidermis the lengths of a number of random line segments are measured. The line segments start at the lower border, are perpendicular to the lower border and end at the opposite border of the mask.

See installation Instructions on the website.

Part of ATLAS software

Comment / Instructions: 

You can upload your image at the Mobyle@SERPICO portal and download the result. The workflow is only available online, i.e. no download possible.

This plugin filters a 3D image stack (or 2D image) to produce a score for how "tube-like" each point in the image is. This is useful as a preprocessing step for tracing neurons or blood vessels, for example. For 3D image stacks, the plugin uses the eigenvalues of the Hessian matrix to calculate this measure of "tubeness", using a metrics mentioned in Sato et al 1997 ¹: if the larger two eigenvalues (λ₂ and λ₃) are both negative then value is √(λ₂λ₃), otherwise the value is 0. For 2D images, if the large eigenvalue is negative, we return its absolute value and otherwise return 0.

This plugin is now bundled as part of Fiji.

The Adipocytes Tools help to analyze fat cells in images from histological section. This is a rather general cell segmentation approach. It can be adapted to different situations via the parameters. This means that you have to find the right parameters for your application.

Sample Image: [0178_x5_3.tif](http://dev.mri.cnrs.fr/attachments/190/0178_x5_3.tif)

Analysis of adipocyte number and size. The original code and example images supposed to be discovered at http://webspace.buckingham.ac.uk/klanglands/ but currently the webpage is missing the code and sample images.