Spatial mapping of molecular profiles of biological tissue samples

A method for spatial detecting nucleic acids in a tissue sample comprising the steps of:

• separating the sample into at least a first layer and a second layer;
• applying at least one imaging label to the first layer;
• imaging the first layer;
• identifying at least one region of interest (ROI) within the sample from the image of the first layer and applying the ROI to the second layer;
• applying at least one species of oligonucleotide probes onto predefined locations within the ROI, said predefined locations defined by a full separation mask, wherein the full separation mask includes a lattice separation mask, and allowing the oligonucleotide probes to bind to the nucleic acids of the sample, wherein the oligonucleotide probes comprise a barcode sequence;
• extracting the nucleic acid-oligonucleotide probes complexes;
• sequencing the extracted nucleic acid molecules;
• correlating the sequenced nucleic acid molecules to the initial location of the corresponding targeted nucleic acid molecules within the ROI to generate a spatial distribution of the targeted nucleic acid molecules, wherein each location is identified by one or more species of oligonucleotide probes bound in the step of applying at least one species of oligonucleotide probes.