ISAS (In Situ Analysis System) is an analysis tool for the temperature and salinity fields. Originally designed for the synthesis of ARGO dataset, it has been tested for the first time on the POMME area in the North-East Atlantic in 2000, it was later extended to the Atlantic and the Global ocean as the Argo array was setting up. It is developed and maintained at LPO (Laboratoire de Physique des Océans) within the Argo Observing Service (SO-ARGO) where it is used for research purposes on ocean variability. ISAS is made available to the Coriolis datacenter for exploitation in operational mode. It can accommodate a wide range of in situ measurements if they are provided in the standard NetCdf format distributed by the Coriolis datacenter (http://www.coriolis.eu.org/ ) . It is based on optimal interpolation and the estimated quantity is the anomaly on depth levels relative to a reference climatology. ISAS is uni-variate, which means that temperature and salinity variables are estimated independently. This document describes the statistical method used to produce the estimate and the specific choices performed to implement the method. The practical implementation and use of the tool is described in the user’s manual corresponding to the appropriate ISAS version.