Devices, systems, and methods for virtual staining

1. A system for virtually staining a tissue sample, the system comprising:

one or more computer readable storage devices configured to store a plurality of computer executable instructions; and

one or more hardware computer processors in communication with the one or more computer readable storage devices and configured to execute the plurality of computer executable instructions in order to cause the system to:

access an electronic medical image of the tissue sample from an electronic data storage medium, the electronic medical image of the tissue sample generated by a hyperspectral detector for detecting electromagnetic radiation directed at the tissue sample by an electromagnetic radiation source, the detected electromagnetic radiation reflected or transmitted from one or more portions of the tissue sample, the electronic medical image of the tissue sample comprising a plurality of pixels generated based on the electromagnetic radiation detected by the hyperspectral detector, wherein the plurality of pixels comprises a first pixel and a second pixel;

determine that a first waveform signature associated with the first pixel of the plurality of pixels is based on a combination of a first plurality of waveform signatures corresponding to multiple substances in the tissue sample at a location associated with the first pixel;

determine the first plurality of waveform signatures;

apply transformation data to the first plurality of waveform signatures in order to obtain a first plurality of outputs;

determine a first single output pixel by volume averaging the first plurality of outputs;

generate a virtually stained first input image of the tissue sample, wherein the virtually stained first input image comprises at least a first single output pixel;

determine that a second waveform signature associated with the second pixel of the plurality of pixels is based on a combination of a second plurality of waveform signatures corresponding to multiple substances in the tissue sample at a location associated with the second pixel;

determine the second plurality of waveform signatures;

apply transformation data to the second plurality of waveform signatures in order to obtain a second plurality of outputs;

determine a second single output pixel by volume averaging the second plurality of outputs;

generate a virtually stained second input image of the tissue sample, wherein the virtually stained second input image comprises at least a second single output pixel;

generate a combined virtually stained image of the tissue sample comprising the virtually stained first input image and the virtually stained second input image; and

display the combined virtually stained image of the tissue sample, wherein the combined virtually stained image is substantially identical to an image of the tissue sample when the tissue sample is treated with an actual stain that corresponds to a virtual stain defined by a virtual staining transform.

2. The system for virtually staining a tissue sample of claim 1 , wherein the tissue sample is in vivo.

3. The system for virtually staining a tissue sample of claim 1 , wherein the tissue sample is in vitro.

4. The system for virtually staining a tissue sample of claim 1 , wherein the determining based on the combination of the first plurality of waveform signatures corresponding to multiple substances in the tissue sample at the location associated with the first pixel and the determining based on the combination of the second plurality of waveform signatures corresponding to multiple substances in the tissue sample at a location associated with the second pixel is based at least in part on a first identified vector signature associated the first pixel of the plurality of pixels and a second identified vector signature associated with the second pixel of the plurality of pixels.

5. The system for virtually staining a tissue sample of claim 1 , wherein the tissue sample is a three-dimensional tissue sample.

6. The system for virtually staining a tissue sample of claim 5 , wherein the hyperspectral detector is configured to change a focal depth to obtain two-dimensional electromagnetic radiation data at varying z depths of the three-dimensional tissue sample.

7. The system for virtually staining a tissue sample of claim 1 , wherein the hyperspectral detector is incorporated into a medical probe.

8. The system for virtually staining a tissue sample of claim 1 , wherein the actual stain is at least one of a dye configured to color certain portions of the tissue sample.

9. The system for virtually staining a tissue sample of claim 1 , wherein the actual stain is a tag.

10. The system for virtually staining a tissue sample of claim 9 , wherein the tag is at least one of an antibody, an aptamer, or a fluorescent protein.

11. A non-transitory electronic storage medium with computer code stored thereon, the computer code configured to virtually stain a tissue sample, and the computer code configured to perform, when executed by a computer processor, the steps of:

access an electronic medical image of the tissue sample from an electronic data storage medium, the electronic medical image of the tissue sample generated by a hyperspectral detector for detecting electromagnetic radiation directed at the tissue sample by an electromagnetic radiation source, the detected electromagnetic radiation reflected or transmitted from one or more portions of the tissue sample, the electronic medical image of the tissue sample comprising a plurality of pixels generated based on the electromagnetic radiation detected by the hyperspectral detector, wherein the plurality of pixels comprises a first pixel and a second pixel;

determine that a first waveform signature associated with the first pixel of the plurality of pixels is based on a combination of a first plurality of waveform signatures corresponding to multiple substances in the tissue sample at a location associated with the first pixel;

determine the first plurality of waveform signatures;

apply transformation data to the first plurality of waveform signatures in order to obtain a first plurality of outputs;

determine a first single output pixel by volume averaging the first plurality of outputs;

generate a virtually stained first input image of the tissue sample, wherein the virtually stained first input image comprises at least the first single output pixel;

determine that a second waveform signature associated with the second pixel of the plurality of pixels is based on a combination of a second plurality of waveform signatures corresponding to multiple substances in the tissue sample at a location associated with the second pixel;

determine the second plurality of waveform signatures;

apply transformation data to the second plurality of waveform signatures in order to obtain a second plurality of outputs;

determine a second single output pixel by volume averaging the second plurality of outputs;

generate a virtually stained second input image of the tissue sample, wherein the virtually stained second input image comprises at least the second single output pixel;

generate a combined virtually stained image of the tissue sample comprising the virtually stained first input image and the virtually stained second input image; and

display the combined virtually stained image of the tissue sample, wherein the combined virtually stained image is substantially identical to an image of the tissue sample when the tissue sample is treated with an actual stain that corresponds to a virtual stain defined by a virtual staining transform.

12. The non-transitory electronic storage medium with computer code stored thereon of claim 11 , wherein the tissue sample is in vivo.

13. The non-transitory electronic storage medium with computer code stored thereon of claim 11 , wherein the tissue sample is in vitro.

14. The non-transitory electronic storage medium with computer code stored thereon of claim 11 , wherein the determining based on the combination of the first plurality of waveform signatures corresponding to multiple substances in the tissue sample at the location associated with the first pixel and the determining based on the combination of the second plurality of waveform signatures corresponding to multiple substances in the tissue sample at a location associated with the second pixel is based at least in part on a first identified vector signature associated the first pixel of the plurality of pixels and a second identified vector signature associated with the second pixel of the plurality of pixels.

15. The non-transitory electronic storage medium with computer code stored thereon of claim 11 , wherein the tissue sample is a three-dimensional tissue sample.

16. The non-transitory electronic storage medium with computer code stored thereon of claim 15 , wherein the hyperspectral detector is configured to change a focal depth to obtain two-dimensional electromagnetic radiation data at varying z depths of the three-dimensional tissue sample.

17. The non-transitory electronic storage medium with computer code stored thereon of claim 11 , wherein the hyperspectral detector is incorporated into a medical probe.

18. The non-transitory electronic storage medium with computer code stored thereon of claim 11 , wherein the actual stain is at least one of a dye configured to color certain portions of the tissue sample.

19. The non-transitory electronic storage medium with computer code stored thereon of claim 11 , wherein the actual stain is a tag.

20. The non-transitory electronic storage medium with computer code stored thereon of claim 19 , wherein the tag is at least one of an antibody, an aptamer, or a fluorescent protein.