Apparatus and method for extended depth of field

A method for extending a depth of field of a nuclei acid sequencer, the method comprising:

• performing a set of optimization steps comprising:
• determining a first result, wherein the first result is a result of passing light emitted by a sample at a nucleic acid site through an objective lens and a mask, wherein the objective lens is focused on a plane which is separated from the nucleic acid site by a target defocus amount, and wherein the mask is disposed between the objective lens and a set of detection pixels;
• determining whether there is a discrepancy between the first result and a second result, wherein the second result is an ideal result for detecting light emitted by the sample at the nucleic acid site;
• and
• based on determining there is the discrepancy between the first result and the second result, performing a set of updating tasks comprising updating the mask based on the determined discrepancy between the first result and the second result;
• and
• repeating the set of optimization steps one or more times.