An instrument for meso-dissection, comprising: a processor; and a memory coupled to the processor, the memory to store computer-readable instructions that, when executed by the processor, cause the processor to perform operations comprising: importing a reference image along with a plurality of annotations, wherein the reference image was digitized from a reference slide scanned on a whole-slide scanner and wherein the annotations were generated using a whole slide viewer interface coupled to the whole-slide scanner; and automatically registering said annotations onto a live capture of a tissue specimen slide to be milled and generating a milling annotation based on said annotations; wherein tissue which is extracted from the tissue specimen slide is dissected based on the annotations, resulting in a milled tissue sample, the instrument further comprising a tracking means for associating the annotations with the milled tissue sample; and wherein the annotations comprise one or more combinations of any geometrical representation depicting one or more regions of interest, characterized in that the operations further comprise associating the annotations and the milled tissue sample with a biological specimen, using a unique identifier at the specimen level and for each tissue slide, and generating a milled annotation based on milled regions of the tissue specimen slide and mapping the milled annotation back to the annotated reference image. a processor; and a memory coupled to the processor, the memory to store computer-readable instructions that, when executed by the processor, cause the processor to perform operations comprising: importing a reference image along with a plurality of annotations, wherein the reference image was digitized from a reference slide scanned on a whole-slide scanner and wherein the annotations were generated using a whole slide viewer interface coupled to the whole-slide scanner; and automatically registering said annotations onto a live capture of a tissue specimen slide to be milled and generating a milling annotation based on said annotations; wherein tissue which is extracted from the tissue specimen slide is dissected based on the annotations, resulting in a milled tissue sample, the instrument further comprising a tracking means for associating the annotations with the milled tissue sample; and wherein the annotations comprise one or more combinations of any geometrical representation depicting one or more regions of interest, characterized in that the operations further comprise associating the annotations and the milled tissue sample with a biological specimen, using a unique identifier at the specimen level and for each tissue slide, and generating a milled annotation based on milled regions of the tissue specimen slide and mapping the milled annotation back to the annotated reference image. importing a reference image along with a plurality of annotations, wherein the reference image was digitized from a reference slide scanned on a whole-slide scanner and wherein the annotations were generated using a whole slide viewer interface coupled to the whole-slide scanner; and automatically registering said annotations onto a live capture of a tissue specimen slide to be milled and generating a milling annotation based on said annotations; wherein tissue which is extracted from the tissue specimen slide is dissected based on the annotations, resulting in a milled tissue sample, the instrument further comprising a tracking means for associating the annotations with the milled tissue sample; and wherein the annotations comprise one or more combinations of any geometrical representation depicting one or more regions of interest, characterized in that the operations further comprise associating the annotations and the milled tissue sample with a biological specimen, using a unique identifier at the specimen level and for each tissue slide, and generating a milled annotation based on milled regions of the tissue specimen slide and mapping the milled annotation back to the annotated reference image.