Data

Through this page, we would like to provide links to open data which may be useful for trying out algorithms or analysis techniques.  Each of these may have particular conditions attached to their use, so please check this carefully for each listed below.

If your research group has a data set that you think may be generally useful for researchers working in neuroinformatics and you would be happy to have it linked to from here, please let us know: ch-node@incf.org

A Focussed Ion Beam (FIB) stack of Rat Striatum

This image data was kindly provided by Graham Knott, head of the BioEM facility at EPFL in Lausanne.  This is a stack of serial images though the striatum of an adult Wistar rat.  The tissue was glutaraldehyde fixed, osmium and uranyl acetate stained, and epoxy resin embedded.  Images were collected in a Zeiss NVision 40 FIB/SEM, with a scale of 5 nm per pixel, z spacing of 9 nm.

You can download the whole stack (in a 1.3GB zip file) or view it interactively using CATMAID:

ssTEM of Layer 4 (Area 17) of the Cat Visual Cortex

This data was kindly provided by Nuno Costa and Kevan A. C. Martin of INI in Zürich. These are TEM serial section micrographs taken from layer 4 of cat visual cortex (area 17). The scale is 1.4 nm per pixel, with z spacing of 40 nm.  These images have been manually annotated in TrakEM2 to show mitochondria and segment individual neurons. If any scientific publications derive from the usage of this data set contact Kevan Martin or Nuno Costa for a citation.

You can download the whole stack, with a TrakEM2 project containing the annotations, or view just the image data using CATMAID:

A Manually Segmented ssTEM Image Stack

Albert Cardona has kindly made available a ssTEM image stack which has cellular features (e.g. cell membranes, mitochondria) marked in complementary label fields.  These are images from the Ventral Nerve Cord (VNC) of a Drosophila first instar larva.  This data may in particular be of use to people studying automated segmentation of TEM images for testing or validation.  For more information, and to download the data, please click on the image below:

Coming Soon

We have two further data sets which will be published here soon - one large Serial Block-Face Scanning Electron Microscope (SBFSEM) stack and an annotated FIB stack.

Other Useful Collections

There is a collection of similar useful data sets available through the Cell Centred Database

website.