Digitally enhanced microscopy for multiplexed histology

A digital stainer system for digitally staining a sample on a microscope slide, comprising:

• an energy emitter positioned to output light towards the sample on the microscope slide held by the digital stainer system, wherein the energy emitter includes a first light source and a second light source;
• an image capture device;
• and
• a controller communicatively coupled to the energy emitter and the image capture device, the controller including at least one processor and memory storing a plurality of digital staining protocols and instructions that, when executed by the at least one processor, cause the digital stainer system to perform a process including:
• capturing, using the image capture device,
• a first image of the sample exposed to a first light waveband from the first light source, and
• a second image of the sample exposed to a second light waveband from the second light source, wherein the second light waveband is different from the first light waveband,
• selecting a digital staining protocol from the plurality of digital staining protocols;
• digitally staining the sample according to the digital staining protocol by
• identifying a first feature of the sample in the first image,
• assigning a first false color to the first feature,
• identifying a second feature of the sample in the second image,
• assigning a second false color to the second feature, and
• generating a digital stained image of the sample with the first false color assigned to the first feature and the second false color assigned to the second feature.

A method for digitally staining a sample on a microscope slide, the method comprising:

• capturing, using an image capture device,
• a first image of the sample exposed to a first light waveband from a first light source, and
• a second image of the sample exposed to a second light waveband from a second light source, wherein the second light waveband is different from the first light waveband,
• selecting a digital staining protocol from a plurality of digital staining protocols;
• digitally staining the sample according to the digital staining protocol by:
• identifying a first feature of the sample in the first image,
• assigning a first false color to the first feature,
• identifying a second feature of the sample in the second image,
• assigning a second false color to the second feature, and
• generating a digital stained image of the sample with the first false color assigned to the first feature and the second false color assigned to the second feature.

A non-transitory computer-readable medium storing instructions that, when executed by a computing system, cause the computing system to perform operations for digitally staining a sample on a microscope slide, the operations comprising:

• capturing, using an image capture device,
• a first image of the sample exposed to a first light waveband from a first light source, and
• a second image of the sample exposed to a second light waveband from a second light source, wherein the second light waveband is different from the first light waveband,
• selecting a digital staining protocol from a plurality of digital staining protocols;
• digitally staining the sample according to the digital staining protocol by:
• identifying a first feature of the sample in the first image,
• assigning a first false color to the first feature,
• identifying a second feature of the sample in the second image,
• assigning a second false color to the second feature, and
• generating a digital stained image of the sample with the first false color assigned to the first feature and the second false color assigned to the second feature.