--- res: bibo_abstract: - Lesion verification and quantification is traditionally done via histological examination of sectioned brains, a time-consuming process that relies heavily on manual estimation. Such methods are particularly problematic in posterior cortical regions (e.g. visual cortex), where sectioning leads to significant damage and distortion of tissue. Even more challenging is the post hoc localization of micro-electrodes, which relies on the same techniques, suffers from similar drawbacks and requires even higher precision. Here, we propose a new, simple method for quantitative lesion characterization and electrode localization that is less labor-intensive and yields more detailed results than conventional methods. We leverage staining techniques standard in electron microscopy with the use of commodity micro-CT imaging. We stain whole rat and zebra finch brains in osmium tetroxide, embed these in resin and scan entire brains in a micro-CT machine. The scans result in 3D reconstructions of the brains with section thickness dependent on sample size (12–15 and 5–6 microns for rat and zebra finch respectively) that can be segmented manually or automatically. Because the method captures the entire intact brain volume, comparisons within and across studies are more tractable, and the extent of lesions and electrodes may be studied with higher accuracy than with current methods.@eng bibo_authorlist: - foaf_Person: foaf_givenName: Javier foaf_name: Masís, Javier foaf_surname: Masís - foaf_Person: foaf_givenName: David foaf_name: Mankus, David foaf_surname: Mankus - foaf_Person: foaf_givenName: Steffen foaf_name: Wolff, Steffen foaf_surname: Wolff - foaf_Person: foaf_givenName: Grigori foaf_name: Guitchounts, Grigori foaf_surname: Guitchounts - foaf_Person: foaf_givenName: Maximilian A foaf_name: Jösch, Maximilian A foaf_surname: Jösch foaf_workInfoHomepage: http://www.librecat.org/personId=2BD278E6-F248-11E8-B48F-1D18A9856A87 orcid: 0000-0002-3937-1330 - foaf_Person: foaf_givenName: David foaf_name: Cox, David foaf_surname: Cox bibo_doi: 10.1038/s41598-018-23247-z bibo_issue: '1' bibo_volume: 8 dct_date: 2018^xs_gYear dct_identifier: - UT:000428234100005 dct_language: eng dct_publisher: Nature Publishing Group@ dct_title: A micro-CT-based method for quantitative brain lesion characterization and electrode localization@ ...