Paparamborde: a software dedicated to quantitative mapping of biological samples using scanning transmission ion microscopy G. Deve `s a, * , C. Michelet-Habchi b , R. Ortega a a Chimie nucle ´aire analytique et bioenvironnementale, UMR 5084 CNRS/Universite ´ de Bordeaux 1, BP 120 Le Haut Vigneau, 33175 Gradignan cedex, France b Centre d’Etudes Nucle ´aire de Bordeaux Gradignan, UMR 5797 CNRS/IN2P3 – Universite ´ de Bordeaux 1, BP 120 Le Haut Vigneau, 33175 Gradignan cedex, France Available online 25 March 2005 Abstract Paparamborde, Programme d’Analyse des PArticules RAlenties dans la Matie `re de BORDEaux, a software dedicated to the scanning transmission ion microscopy (STIM) analysis of biological samples was developed. The programme includes the reconstruction of the median and/or mean energy loss image of the sample, as well as accurate calculation of sample thickness performed over the whole or a part of the scanned surface. The calculation is based on the conver- sion of transmitted particle energy into areal density of matter (lg/cm 2 ) and uses SRIM code for the stopping power calculation. A new routine for the calculation of X-ray absorption correction factors (XCF), as needed for PIXE quan- tification of trace element, has been added in the latest version of Paparamborde, allowing the thickness heterogeneity of sample to be properly taken into account in the calculation of XCF. Ó 2005 Elsevier B.V. All rights reserved. PACS: 29.50; 07.78; 07.79; 82.80 Keywords: Scanning transmission ion microscopy; Quantitative analysis; Biological samples; Data analysis 1. Introduction The microanalysis of biological samples using nuclear microprobe techniques, micro-PIXE (par- ticle induced X-ray emission), micro-RBS (Ruther- ford backscattering spectrometry) and STIM (scanning transmission ion microscopy), is now 0168-583X/$ - see front matter Ó 2005 Elsevier B.V. All rights reserved. doi:10.1016/j.nimb.2005.01.047 * Corresponding author. Tel.: +33 557 120 903; fax: +33 557 120 900. E-mail address: deves@cenbg.in2p3.fr (G. Deve `s). Nuclear Instruments and Methods in Physics Research B 231 (2005) 136–141 www.elsevier.com/locate/nimb