Parallel imaging acquisition and restoration methods and systems

1. An imaging system comprising:

an illumination system having an array of light sources configured to sequentially activate different subsets of light sources in the array to provide a plurality of illumination patterns incident one or more sample wells;

an optical system configured to focus light transmitted through the one or more sample wells;

one or more sets of image sensors, each set configured to receive light focused by the optical system from one sample well of the one or more sample wells and configured to acquire a plurality of raw images, each raw image acquired while illumination of one of the illumination patterns is incident at least the one sample well;

one or more multiplexers, each multiplexer in communication with one set of the one or more sets of image sensors, each multiplexer and configured to forward raw images acquired by the one set of image sensors;

an internal memory comprising an in-memory parallel system;

a hard drive; and

a plurality of processors comprising at least a first processor and a second processor, each processor in read/write communication with the memory and in communication with one of the multiplexers, each processor configured to: (i) perform sorting, segmenting, and indexing of the plurality of raw images incoming from each image sensor of the one set of image sensors to a four-dimensional hypercube formed in the in-memory parallel system and (ii) write segments of the four-dimensional hypercube to memory blocks on the hard drive,

the plurality of processors comprising a first processor, a second processor and a third processor, the first processor configured to import memory blocks for a first tile while the second processor reconstructs an improved resolution image for a second tile using a reconstruction process and while the third processor writes an improved resolution image for a third tile to the hard drive.

2. The imaging system of claim 1 , wherein the segments of the four-dimensional hypercube are linked to memory blocks on the hard drive.

3. The imaging system of claim 1 , wherein the one or more sample wells are in a multi-well plate loaded into the imaging system during operation.

4. The imaging system of claim 1 , wherein the plurality of processors are further configured to perform a cascading, parallel restoration operation to generate an improved resolution image for each of the one or more sample wells based on the plurality of raw images acquired for the respective well based on the plurality of illumination patterns.

5. The imaging system of claim 1 ,

wherein each of the plurality of processors is configured to import memory blocks for one tile, to reconstruct an improved resolution image for the one tile using the reconstruction process, and to write the improved resolution image for the one tile for the one or more sets of image sensors to the hard drive.

6. The imaging system of claim 5 , wherein each of the plurality of processors is configured to import, reconstruct, and write in a cascading manner.

7. The imaging system of claim 1 , wherein the plurality of processors are further configured to discard one or more of the plurality of raw images before performing sorting, segmenting, and indexing of the plurality of raw images.

8. The imaging system of claim 1 , wherein a master processor of the plurality of processors is configured to sequentially active different subsets of the light sources to provide the plurality of illumination patterns incident the one or more sample wells and activate the one or more sets of image sensors to acquire one of the plurality of images while light from one of the illumination patterns is incident the one or more sample wells.

9. An imaging method comprising:

sequentially activating different subsets of light sources in an array of light sources to sequentially provide a plurality of illumination patterns of illumination incident one or more sample wells;

acquiring, by each set of one or more sets of image sensors, a plurality of raw images, each raw image acquired while illumination of one of the illumination patterns is incident the one or more sample wells;

sorting, segmenting, and indexing of the plurality of raw images incoming from each set of the one or more sets of image sensors to a four-dimensional hypercube formed in an in-memory parallel system;

writing segments of the four-dimensional hypercube to linked memory blocks on a hard drive; and

importing, with a first processor, memory blocks for a first tile from the hard drive while a second processor reconstructs an improved resolution image for a second tile using a reconstruction process and while a third processor writes an improved resolution image for a third tile to the hard drive.

10. The imaging method of claim 9 , further comprising linking segments of the four-dimensional hypercube to memory blocks on the hard drive.

11. The imaging method of claim 9 , further comprising loading a multi-well plate with the one or more sample wells.

12. The imaging method of claim 9 , further comprising performing a cascading, parallel restoration operation to generate an improved resolution image for each of the one or more sample wells using image data from the plurality of raw images acquired for the respective well based on the plurality of illumination patterns.

13. The imaging method of claim 9 , further comprising discarding one or more of the plurality of raw images before performing sorting, segmenting, and indexing of the plurality of raw images.

14. The imaging method of claim 9 , further comprising multiplexing the plurality of raw images from each of the one or more sets of the image sensors to one of the plurality of processors.