Systems and methods for imaging samples with reduced sample motion artifacts
Systems and methods to identify and/or reduce or eliminate sample motion artifacts are disclosed. Sample motion artifacts may be reduced or eliminated using scan patterns where an acquisition time difference between when perimeter pixels in adjacent tiles are acquired is reduced, as compared to a conventional raster scan to reduce or eliminate discontinuities that would otherwise appear at tile boundaries in an image. In some embodiments, test images acquired using relatively small test scan patterns or intensities of test points acquired at different times may be compared to determine whether sample motion has occurred. In some embodiments, intensity of adjacent pixels at a tile boundary are compared. In some embodiments, intensity of one or more single pixels is monitored over time to determine whether sample motion has occurred over a period of time. In some embodiments, a flattening or reshaping tool may be used to suppress sample motion during imaging.
1. A method of imaging a sample using an array of micro optical elements, the method comprising:
scanning the array of micro optical elements along a scan pattern defined by an array of sequential positions to generate an image of the sample, wherein the array of sequential positions is an M×N array, M and N are each no less than 10, and M≥N;
wherein the image comprises tiles of pixels, the tiles each corresponding to a respective micro optical element in the array and the pixels each corresponding to a position in the array of sequential positions,
wherein, for each pair of a first pixel in a first one of the tiles and a second pixel adjacent to the first pixel, the second pixel being in a different one of the tiles than the first one of the tiles, a position difference between the position corresponding to the first pixel and the position corresponding to the second pixel is less than (MN−2M+1).
2. The method of claim 1 , wherein a position difference in the sequence of scan positions of a scan pattern between the position corresponding to the first pixel and the position corresponding to the second pixel is no more than (3M−3).
3. The method of claim 1 , wherein a position difference in the sequence of scan positions of a scan pattern between the position corresponding to the first pixel and the position corresponding to the second pixel is no more than (2M−1).
4. The method of claim 1 , wherein for each pair of adjacent pixels belonging to the same one tile, a position difference in the sequence of scan positions of a scan pattern between the position corresponding to the first pixel and the position corresponding to the second pixel is no more than (2M+2N−5).
5. The method of claim 1 , wherein for each pair of adjacent pixels belonging to the same one tile, a position difference in the sequence of scan positions of a scan pattern between the position corresponding to the first pixel and the position corresponding to the second pixel is no more than (2M).
6. The method of claim 1 , wherein for each pair of a first pixel in a first one of the tiles and a second pixel adjacent to the first pixel, the second pixel being in a different one of the tiles than the first one of the tiles, a position difference between the position corresponding to the first pixel and the position corresponding to the second pixel is less than 30% of the total number of scan positions in the scan pattern.
7. The method of claim 1 , wherein for each pair of adjacent pixels belonging to the same one tile, a position difference between the position corresponding to the first pixel and the position corresponding to the second pixel is less than 30% of the total number of scan positions in the scan pattern.
8. The method of claim 1 , wherein the array of sequential positions forms a spiral.
9. The method of claim 1 , wherein the array of sequential positions is a regular array.
10. The method of claim 1 , wherein the scan pattern has a size corresponding to a size of a unit cell of a micro optical element in the array of micro optical elements.
11. The method of claim 1 , comprising, during the scanning, (i) providing illumination light to the sample through the micro optical elements and (ii) collecting corresponding back-emitted light from the sample with the micro optical elements that is subsequently received at a detector.
12. The method of claim 11 , comprising generating, by a processor of a computing device, the image of the sample based on the corresponding back-emitted light received at the detector.
13. The method of claim 1 , wherein the series of sequential positions comprises a series of sequential rows of positions, wherein each of the sequential rows in the series is temporally separated from its spatially adjacent rows in the series by no more than two rows in the series.
14. The method of claim 13 , wherein a starting position of the scan pattern is in an interior one of the sequential rows of positions and a final position of the scan pattern is in an exterior one of the sequential rows of positions.
15. The method of claim 14 , wherein each row in the series of sequential rows of positions is no closer to the interior one of the sequential rows of positions than an immediately preceding row in the series of sequential rows of positions.
16. The method of claim 13 , wherein a starting position of the scan pattern is in an exterior one of the sequential rows of positions and a final position of the scan pattern is in an interior one of the sequential rows of positions.
17. The method of claim 16 , wherein each row in the series of sequential rows of positions is no further from the interior one of the sequential rows of positions than an immediately preceding row in the series of sequential rows of positions.
18. The method of claim 13 , wherein the scan pattern is unidirectional.
19. The method of claim 13 , wherein the scan pattern is bidirectional.