(a) compartmentalizing said sample with a grid into at least two compartments, wherein the grid comprises at least two break-through holes which define said at least two compartments of the sample and wherein at least one of said at least two compartments of the sample comprises at least one cell containing a plurality of molecules;

(b) labeling the plurality of molecules within said at least one cell in situ with at least a compartment-specific label,

wherein before step (a) the sample is fixed and permeabilized, and wherein steps (a) and (b) are performed repeatedly and alternating, wherein before every repetition of step (a) at least one of the following steps is performed:

rotating the grid in relation to the surface defined by the two largest dimensions of the sample around an axis perpendicular to said surface;

rotating the grid in relation to said surface around an axis parallel to said surface;

shifting the grid in relation and parallel to said surface;

exchanging the grid by a further grid, wherein said further grid comprises at least two break-through holes which differ with respect to their number and/or at least one cross-sectional size and/or at least one cross-sectional geometry from the at least two break-through holes of any of the at least one grid applied in any of the previous steps (a);

choosing one of the at least one grid applied in any of the previous steps (a);

(c) obtaining a single cell suspension from the compartmentalized sample comprising the compartment-specific labeled molecules within the cell(s);

(d) mixing at least a fraction of said single cell suspension and distributing it over at least two vessels;

(e) labeling within the at least two vessels the plurality of molecules within the cell(s) with a vessel-specific label; and

(f) obtaining data for at least a fraction of the sequence of at least a fraction of the plurality of molecules, said data being obtained using a sequencing or genotyping method or a next generation sequencing method.