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The cytosolic concentration of free calcium ions (<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mrow><mo>[</mo><msup><mi>Ca</mi><mrow><mn>2</mn><mo>+</mo></mrow></msup><mo>]</mo></mrow></semantics></math></inline-formula>) is an important intracellular messenger in most cell types, and the spatial distribution of <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mrow><mo>[</mo><msup><mi>Ca</mi><mrow><mn>2</mn><mo>+</mo></mrow></msup><mo>]</mo></mrow></semantics></math></inline-formula> is often critical. In a salivary gland acinar cell, a polarised epithelial cell, whose principal function is to transport water and thus secrete saliva, <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mrow><mo>[</mo><msup><mi>Ca</mi><mrow><mn>2</mn><mo>+</mo></mrow></msup><mo>]</mo></mrow></semantics></math></inline-formula> controls the secretion of primary saliva, but increases in <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mrow><mo>[</mo><msup><mi>Ca</mi><mrow><mn>2</mn><mo>+</mo></mrow></msup><mo>]</mo></mrow></semantics></math></inline-formula> are localised to the apical regions of the cell. Hence, any quantitative explanation of how <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mrow><mo>[</mo><msup><mi>Ca</mi><mrow><mn>2</mn><mo>+</mo></mrow></msup><mo>]</mo></mrow></semantics></math></inline-formula> controls saliva secretion must take into careful account the spatial distribution of the various <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msup><mi>Ca</mi><mrow><mn>2</mn><mo>+</mo></mrow></msup></semantics></math></inline-formula> sources, <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msup><mi>Ca</mi><mrow><mn>2</mn><mo>+</mo></mrow></msup></semantics></math></inline-formula> sinks, and <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msup><mi>Ca</mi><mrow><mn>2</mn><mo>+</mo></mrow></msup></semantics></math></inline-formula>-sensitive ion channels. Based on optical slices, we have previously constructed anatomically accurate three-dimensional models of seven salivary gland acinar cells, and thus shown that a model in which <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msup><mi>Ca</mi><mrow><mn>2</mn><mo>+</mo></mrow></msup></semantics></math></inline-formula> responses are confined to the apical regions of the cell is sufficient to provide a quantitative and predictive explanation of primary saliva secretion. However, reconstruction of such anatomically accurate cells is extremely time consuming and inefficient. Here, we present an alternative, mostly automated method of constructing three-dimensional cells that are approximately anatomically accurate and show that the new construction preserves the quantitative accuracy of the model.