Preparation of tissue sections using fluorescence-based detection

1. A method of determining a location of a tissue in an embedded sample, the method comprising:

irradiating an embedded sample with light having a wavelength of from about 200 nm to about 600 nm, wherein the embedded sample comprises a tissue and an embedding medium;

detecting endogenous fluorescence emission of the embedded sample; and

determining a location of at least a portion of the tissue in the embedded sample based on the endogenous fluorescence emission;

obtaining a slice comprising at least a portion of the tissue in the embedded sample; and

analyzing the slice.

2. The method of claim 1 , wherein the embedding medium is a paraffin.

3. The method of claim 1 , wherein the embedded sample is a formalin-fixed paraffin-embedded (FFPE) tissue block.

4. The method of claim 1 , wherein the endogenous fluorescence emission is detected using an imaging device comprising a camera.

5. The method of claim 4 , wherein a digital image of the endogenous fluorescence emission is used to determine the location of the portion of the tissue in the embedded sample.

6. The method of claim 5 , wherein pixel intensity of the digital image is used to determine the location of the portion of the tissue in the embedded sample.

7. The method of claim 1 , wherein the method is used to determine location of a tissue surface.

8. The method of claim 7 , further comprising slicing or trimming a section from the embedded sample after determining the location of the tissue surface.

9. An apparatus for slicing a tissue section from an embedded sample, the apparatus comprising:

a microtome comprising a sample holder;

at least one light source directed at the sample holder;

an optical system positioned to capture endogenous emitted light from a sample held by the sample holder; and

a processor in communication with the optical system and configured to provide a signal based on an endogenous fluorescence emission from the sample and to determine a location of the tissue section of the embedded sample based on the endogenous fluorescence emission.

10. The apparatus of claim 9 , further comprising a dichroic beam splitter.

11. The apparatus of claim 10 , wherein the dichroic beam splitter is part of a filter cube.

12. The apparatus of claim 9 , wherein the optical system comprises a fluorescence microscope or a camera.

13. The apparatus of claim 9 , wherein the apparatus comprises at least two light sources.

14. The apparatus of claim 9 wherein the at least one light source is selected from the group consisting of an LED light source, a mercury arc lamp, a Xenon arc lamp, and a laser.

15. The method of claim 1 , wherein the embedding medium comprises paraffin, a blend of fully refined paraffin wax and a synthetic resin or polymer, or an epoxy resin.

16. The apparatus of claim 1 , wherein the embedding medium comprises a fully refined paraffin wax.

17. The apparatus of claim 1 , wherein the embedding medium comprises an epoxy resin.

18. The method of claim 1 , wherein the epoxy resin comprises a glycidyl epoxy resin or a non-glycidyl epoxy resin.

19. The apparatus of claim 18 , wherein the non-glycidyl epoxy resin comprises an aliphatic resin or an cyclo-aliphatic resin.

20. A method of trimming an embedded tissue sample until the surface of the tissue is found, the method comprising:

irradiating an embedded tissue sample with light having a wavelength of from about 200 nm to about 600 nm, wherein the embedded sample comprises a tissue and an embedding medium;

detecting endogenous fluorescence emission of the embedded sample;

analyzing the endogenous fluorescence emission;

cutting or slicing the embedded tissue sample to provide a slice and a trimmed block; and

repeating the cutting or slicing process until a surface of the tissue is found.