A method for measuring the concentrations of at least one metabolic gas emitted by microorganisms or living cells in biological material in a container, the method comprising: - applying non-invasive in-situ optical measurements to a region of interest being a dead space free of a biological material and in a fluid communication with a portion of the container containing the biological material, wherein said optical measurements comprise illuminating said region of interest with light of a predetermined spectrum including at least first and second predetermined wavelengths of substantially narrow spectra corresponding to respectively an absorption peak of at least one metabolic gas and a spectral region outside the absorption peak of said at least one metabolic gas, and measuring transmission of said first and second wavelengths through said dead space; and - analyzing measured data of said transmission and generating data indicative of a concentration of the at least one metabolic gas in said dead space which is in the fluid communication with the biological material, said generated data being thereby indicative of microorganisms in the biological material, wherein said determining of the concentration of at least one metabolic gas comprises: (i) measuring IR transmission through the dead space in two or more wavelengths comprising said first and second wavelengths, said measuring comprising: (a) tuning a central wavelength of illuminating light each one of said two or more wavelengths, (b) detecting IR light in said two or more wavelengths transmitted through the dead space, and (c) generating measured data indicative of two or more intensity values comprising first and second intensity values corresponding to the light transmitted through the dead space in said first and second wavelengths for a given optical path defined by the optical system and the dead space; and (ii) processing the measured data based on an absorption model of the at least one metabolic gas, said processing comprising determining a best fit between intensity values obtained from said absorption model and said measured intensity values, to thereby determine the concentration of said at least one metabolic gas. - applying non-invasive in-situ optical measurements to a region of interest being a dead space free of a biological material and in a fluid communication with a portion of the container containing the biological material, wherein said optical measurements comprise illuminating said region of interest with light of a predetermined spectrum including at least first and second predetermined wavelengths of substantially narrow spectra corresponding to respectively an absorption peak of at least one metabolic gas and a spectral region outside the absorption peak of said at least one metabolic gas, and measuring transmission of said first and second wavelengths through said dead space; and - analyzing measured data of said transmission and generating data indicative of a concentration of the at least one metabolic gas in said dead space which is in the fluid communication with the biological material, said generated data being thereby indicative of microorganisms in the biological material, wherein said determining of the concentration of at least one metabolic gas comprises: (i) measuring IR transmission through the dead space in two or more wavelengths comprising said first and second wavelengths, said measuring comprising: (a) tuning a central wavelength of illuminating light each one of said two or more wavelengths, (b) detecting IR light in said two or more wavelengths transmitted through the dead space, and (c) generating measured data indicative of two or more intensity values comprising first and second intensity values corresponding to the light transmitted through the dead space in said first and second wavelengths for a given optical path defined by the optical system and the dead space; and (ii) processing the measured data based on an absorption model of the at least one metabolic gas, said processing comprising determining a best fit between intensity values obtained from said absorption model and said measured intensity values, to thereby determine the concentration of said at least one metabolic gas. (i) measuring IR transmission through the dead space in two or more wavelengths comprising said first and second wavelengths, said measuring comprising: (a) tuning a central wavelength of illuminating light each one of said two or more wavelengths, (b) detecting IR light in said two or more wavelengths transmitted through the dead space, and (c) generating measured data indicative of two or more intensity values comprising first and second intensity values corresponding to the light transmitted through the dead space in said first and second wavelengths for a given optical path defined by the optical system and the dead space; and (a) tuning a central wavelength of illuminating light each one of said two or more wavelengths, (b) detecting IR light in said two or more wavelengths transmitted through the dead space, and (c) generating measured data indicative of two or more intensity values comprising first and second intensity values corresponding to the light transmitted through the dead space in said first and second wavelengths for a given optical path defined by the optical system and the dead space; and (ii) processing the measured data based on an absorption model of the at least one metabolic gas, said processing comprising determining a best fit between intensity values obtained from said absorption model and said measured intensity values, to thereby determine the concentration of said at least one metabolic gas.