Visualization and measurement of cell compartments
The disclosure features methods and systems that include a detector configured to obtain multiple images of a sample stained with first and second stains, where the first and second stains have similar spectral absorption and emission profiles, and an electronic processor configured to decompose the multiple images into an unmixed image set, where the unmixed image set includes a first unmixed image corresponding to the first stain and a second unmixed image corresponding to the second stain, and identify nuclear regions in the sample based on the first unmixed image and identify cytoplasm regions in the sample based on the second unmixed image.
1. A system, comprising:
a detector configured to obtain multiple images of a sample stained with first and second counterstains, wherein the first and second counterstains have similar spectral absorption and emission profiles; and
an electronic processor configured to:
decompose the multiple images into an unmixed image set, wherein the unmixed image set comprises a first unmixed image corresponding to the first counterstain and a second unmixed image corresponding to the second counterstain; and
identify nuclear regions in the sample based on the first unmixed image and identify cytoplasm regions in the sample based on the second unmixed image.
2. The system of claim 1 , wherein the electronic processor is further configured to generate an image of the sample, and wherein the nuclear and cytoplasm regions in the image are colored in the same manner as if the sample was stained with hematoxylin and eosin.
3. The system of claim 1 , wherein the sample comprises one or more immunofluorescent probes, and wherein the unmixed image set comprises unmixed images that each correspond to contributions from only one of the immunofluorescent probes.
4. The system of claim 3 , wherein the electronic processor is further configured to determine an amount of at least some of the immunofluorescent probes in the nuclear and cytoplasm regions in the sample.
5. The system of claim 3 , wherein the sample comprises at least three immunofluorescent probes.
6. The system of claim 3 , wherein the sample comprises at least five immunofluorescent probes.
7. The system of claim 1 , wherein the multiple images comprise fluorescence images.
8. The system of claim 1 , wherein the second stain is CellMask Blue.
9. The system of claim 8 , wherein the first stain is DAPI.
10. The system of claim 8 , wherein the first stain is Hoechst 33258.
11. The system of claim 1 , wherein the multiple images define an image cube.
12. The system of claim 1 , wherein each of the multiple images corresponds to a fluorescence image of the sample for a different corresponding range of fluorescence wavelengths.
13. The system of claim 1 , further comprising a multi-spectral imaging system coupled to the detector, wherein the multi-spectral imaging system is configured to illuminate the sample to obtain the multiple images.
14. A method, comprising:
applying at least two counterstains to a sample, wherein the at least two counterstains have similar spectral absorption and emission profiles; and
using an electronic processor to:
obtain multiple images of the sample;
obtain a first unmixed image corresponding to a first one of the counterstains and a second unmixed image corresponding to a second one of the counterstains; and
identify nuclear regions in the sample based on the first unmixed image and identify cytoplasm regions in the sample based on the second unmixed image.
15. The method of claim 14 , further comprising using the electronic processor to:
decompose the multiple images into an unmixed image set, wherein the unmixed image set comprises the first unmixed image and the second unmixed image.
16. The method of claim 15 , further comprising using the electronic processor to generate an image of the sample, wherein the nuclear and cytoplasm regions in the image are colored in the same manner as if the sample was stained with hematoxylin and eosin.
17. The method of claim 15 , wherein the sample comprises one or more immunofluorescent probes, and wherein the unmixed image set comprises unmixed images that each correspond to contributions from only one of the immunofluorescent probes.
18. The method of claim 17 , further comprising using the electronic processor to determine an amount of at least some of the immunofluorescent probes in the nuclear and cytoplasm regions in the sample.
19. The method of claim 17 , wherein the sample comprises at least three immunofluorescent probes.
20. The method of claim 17 , wherein the sample comprises at least five immunofluorescent probes.
21. The method of claim 15 , wherein the multiple images comprise fluorescence images.
22. The method of claim 14 , wherein the at least two stains comprise CellMask Blue and DAPI.
23. The method of claim 14 , wherein the at least two stains comprise CellMask Blue and Hoechst 33258.
24. The method of claim 14 , wherein the multiple images define an image cube.
25. The method of claim 14 , wherein each of the multiple images corresponds to a fluorescence image of the sample for a different corresponding range of fluorescence wavelengths.
26. A system, comprising:
a detector configured to obtain multiple images of a sample stained with first and second stains, wherein the first stain comprises DAPI or Hoeschst 33258 and the second stain comprises CellMask Blue; and
an electronic processor configured to:
decompose the multiple images into an unmixed image set, wherein the unmixed image set comprises a first unmixed image corresponding to the first stain and a second unmixed image corresponding to the second stain; and
identify nuclear regions in the sample based on the first unmixed image and identify cytoplasm regions in the sample based on the second unmixed image.
27. The system of claim 26 , wherein the electronic processor is further configured to generate an image of the sample, and wherein the nuclear and cytoplasm regions in the image are colored in the same manner as if the sample was stained with hematoxylin and eosin.
28. The system of claim 26 , wherein the sample comprises one or more immunofluorescent probes, and wherein the unmixed image set comprises unmixed images that each correspond to contributions from only one of the immunofluorescent probes.
29. The system of claim 28 , wherein the electronic processor is further configured to determine an amount of at least some of the immunofluorescent probes in the nuclear and cytoplasm regions in the sample.
30. A method, comprising:
applying at least two stains to a sample, wherein the first stain comprises DAPI or Hoeschst 33258 and the second stain comprises CellMask Blue; and
using an electronic processor to:
obtain multiple images of the sample;
obtain a first unmixed image corresponding to the first stain and a second unmixed image corresponding to the second stain; and
identify nuclear regions in the sample based on the first unmixed image and identify cytoplasm regions in the sample based on the second unmixed image.
31. The method of claim 30 , further comprising using an electronic processor to:
decompose the multiple images into an unmixed image set, wherein the unmixed image set comprises the first unmixed image and the second unmixed image.
32. The method of claim 31 , further comprising using the electronic processor to generate an image of the sample, wherein the nuclear and cytoplasm regions in the image are colored in the same manner as if the sample was stained with hematoxylin and eosin.
33. The method of claim 31 , wherein the sample comprises one or more immunofluorescent probes, and wherein the unmixed image set comprises unmixed images that each correspond to contributions from only one of the immunofluorescent probes.
34. The method of claim 33 , further comprising using the electronic processor to determine an amount of at least some of the immunofluorescent probes in the nuclear and cytoplasm regions in the sample.