Tissue sample preparation system

1. A method of preparing a biological tissue sample for optical analysis such that a deviation of a volume, a morphology, or both a volume and a morphology of a prepared sample from a volume or a morphology of an original tissue is reduced, the method comprising:

a) fixing the tissue sample with a first fixation solution;

b) immersing the fixed tissue sample in a delipidation solution, the delipidation solution including,

a chaotropic agent configured to induce a swelling of the sample;

d) staining the tissue sample with one or more staining solutions;

f) dehydrating the stained tissue sample in an organic dehydration solution, the dehydration solution configured to induce a shrinking of the sample; and

g) immersing the fixed tissue sample in an organic clearing solution, wherein the delipidation solution is a water-based clearing solution.

2. The method of claim 1 , further comprising:

c) illuminating the sample with light of a wave length range comprising emission, excitation, or both emission and excitation wave lengths of the stain in order to selectively remove or reduce autofluorescence of the sample in said wave length range.

3. The method of claim 1 , further comprising:

e) fixing the stained tissue sample with a second fixation solution before the washing and dehydration is performed.

4. The method of claim 1 , wherein a composition of the delipidation solution is chosen such that the tissue shrinkage induced by the organic dehydration solution is compensated in advance by the swelling induced by the delipidation solution.

5. The method of claim 1 ,

wherein the chaotropic agent is configured to cause a swelling of the volume of the sample by at least 15% of the volume of the original sample, or by at least 20% of the volume of the original sample; or

wherein a composition of the delipidation solution is chosen such that a combined effect of the swelling induced by the delipidation solution and of the shrinking induced by the dehydration solution provides a cleared tissue sample that deviates from the volume of the original, untreated tissue sample by less than 15%.

6. The method of claim 1 , the chaotropic agent being a non-ionic chaotropic agent, urea or thio-urea, or an ionic chaotropic agent guanidinium including a guanidinium salt.

7. The method of claim 1 , wherein the delipidation solution comprises 5-30%, 10-25%, 15-25%, or 20-25% by volume an amino alcohol including N,N,N′,N′, tetrakis (2-hydroxypropyl)ethyl-enediamine.

8. The method of claim 1 , wherein the fixing of the tissue in the first fixation solution, the immersing of the fixed tissue sample in the delipidation solution, the staining, dehydrating and the immersing of the fixed tissue sample in the organic clearing solution are performed in an automated or a semi-automated process, the automated or the semi-automated process being free of a perfusion.

9. The method of claim 1 , wherein

the organic clearing solution is a mixture of benzyl alcohol and benzyl benzoate (BABB), and

the method further comprises:

preparing the organic clearing solution, the preparing comprising choosing a ratio of benzyl alcohol and benzyl benzoate such that a refractive index of the organic clearing solution is identical to a refractive index of the tissue type of the sample.

10. The method of claim 1 , wherein the sample has a volume of at least 0.5 cm 3 , of at least 0.75 cm 3 , or of at least 1 cm 3 .

11. The method of claim 1 , wherein the sample comprises

a reporter protein or a stained biomarker, drug or metabolite already before the sample is fixed with the first fixation solution.

12. The method of claim 1 , further comprising:

generating a 3D plot of stained sub-structures of the cleared tissue sample using a light-sheet fluorescence microscope.

13. An automated or semi-automated system for preparing a biological tissue sample for optical analysis, the system being configured for:

receiving a fixed tissue sample, the fixed tissue sample having been fixed with a first fixation solution;

immersing the fixed tissue sample in a delipidation solution, the delipidation solution comprising a chaotropic agent configured to induce a swelling of the sample;

staining the tissue sample with one or more staining solutions;

washing and dehydrating the stained tissue sample in an organic dehydration solution, the dehydration solution configured to induce a shrinking of the sample; and

immersing the fixed tissue sample in an organic clearing solution, wherein the delipidation solution is a water-based clearing solution.

14. The automated or semi-automated system of claim 13 , wherein

the system comprises a reagent container for each one of a plurality of solutions comprising a delipidation solution, one or more staining solutions, a second fixation solution, an organic dehydration solution and an organic clearing solution;

the system comprises a sample transport means and a plurality of sample containers respectively being coupled to one of the reagent containers, the system being configured to coordinate the sample transport semi-automatically or fully automatically such that the sample is immersed in each of the plurality of solutions at least once in accordance with claim 13 ; or

the system comprises one or more pumps respectively being coupled to one of the reagent containers and to a sample container, the system being configured to coordinate the pumps such that the sample is immersed in each of the plurality of solutions at least once in accordance with claim 13 .

15. A kit for preparing one or more tissue samples comprising:

a water-based delipidation solution comprising:

5%-30% or 5%-15% by volume of at least one chaotropic agent;

5-30% by volume of at least one detergent;

and

an organic clearing solution.

16. The kit of claim 15 , wherein the chaotropic agent is a non-ionic chaotropic agent or guanidinium including a guanidinium salt.

17. The kit of claim 15 , wherein the chaotropic agent is urea or thio-urea.

18. The kit of claim 15 , wherein the delipidation solution further comprises 5-30%, 10-25%, 15-25%, or 20-25% by volume of an amino alcohol, the amino alcohol including N,N,N′,N′, tetrakis(2-hydroxypropyl)ethylenediamine.

19. The kit of claim 15 , wherein the at least one detergent is a combination of at least two different detergents, the combination including triethanol amin (TEA) and Tween-80.

20. The method of claim 5 , wherein the delipidation solution comprises 5%-30% by volume of at least one chaotropic agent.