Methods and systems for counting nuclei for cells in a cell-containing sample are disclosed, such as carried out on a computer. The methods comprise: receiving a raw image of the cell-containing sample; transforming the raw image into a segmented image comprising one or more nuclei clusters. The methods further comprise: for each of the one or more nuclei clusters, obtaining a convex hull of the nuclei cluster; locating any indentations on the nuclei cluster by comparing the nuclei cluster to the convex hull of the nuclei cluster; calculating a first nuclei count based on a tally of the indentations; and assigning the nuclei cluster to a cell among the plurality of cells. The methods further comprise: calculating a second nuclei count for each cell by totaling the first nuclei counts of its constituent nuclei clusters; and presenting a result based on the second nuclei count for at least one of the plurality of cells.