Public data sets

Revision as of 06:49, 6 April 2010 by Albertcardona (talk | contribs) (Added migrating macrophages data set)

Do you need image data to try your algorithms on? Do you lack expert ground truth to test your methods? No problem! Here you have a list of available public data sets from the Fiji community and other sources:

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30 sections from a serial section Transmission Electron Microscopy (ssTEM) data set of the Drosophila first instar larva ventral nerve cord (VNC). The microcube measures 2 x 2 x 1.5 microns approx., with a resolution of 4x4x50 nm/pixel.
The challenge: use this data set to train machine learning software for the purpose of automatic segmentation of neural structures in ssTEM.
The images are representative of actual images in the real-world: there is a bit of noise; there are image registration errors; there is even a small stitching error in one section. None of these led to any difficulties in the manual labeling of each element in the image stack by an expert human neuroanatomist. A software application that aims at removing or reducing human operation must be able to cope with all these issues.
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The dataset consists of tubulin histone GFP coexpressing C. elegans embryos. All image planes were collected at 512x512 resolution in 8-bit grayscale.
4D data set, kindly provided by Dirk Sieger and Francesca Peri, EMBL.
Migrating-macrophages.gif
The challenge: trace the macrophages in 4D, and measure their shape volumes, surfaces, positions and pixel value intensities.
The file is a tif hyperstack that can be loaded directly into the 3D Viewer.