Reconstruction of a distorted image of an array of structural elements of a specimen

A method, comprising:

• receiving a warped image of an array of cells of a specimen, wherein each cell of the array comprises one or more structural elements of a substrate;
• generating a reference image of a region associated with a cell of the array of cells;
• identifying a first cell of the array of cells using the reference image and at least part of the warped image;
• identifying one or more locations comprising cells that differ from the first cell;
• determining, based at least on the one or more locations, a warped compensation transform;
• and
• applying the warped compensation transform on the warped image to generate an undistorted image.

A non-transitory computer readable storage medium comprising instructions that, when executed by a processing device, cause the processing device to perform operations comprising:

• receiving a warped image of an array of cells of a specimen, wherein each cell of the array comprises one or more structural elements of a substrate;
• generating a reference image of a region associated with a cell of the array of cells;
• identifying a first cell of the array of cells using the reference image and at least part of the warped image;
• identifying one or more locations comprising cells that differ from the first cell;
• determining, based at least on the one or more locations, a warped compensation transform;
• and
• applying the warped compensation transform on the warped image to generate an undistorted image.