Abstract : Capsule Counts with precision comparable to those of an expert observer can be achieved automatically. Aims To develop an open-source freeware program that automatically extracts and counts the number of birds in aerial images of dense aggregations. Methods Software was developed and validated using aerial photographs of Greater Flamingo colonies from France, Turkey and Mauritania. We used a stochastic approach based on object processes. The objects representing flamingos were defined as ellipses, and the software detected these and produced a count. Details of the procedure are provided in electronic supplementary material. The energy is extracted by a birth-and-death algorithm, leading to the total number of birds. Results This procedure gave counts with precision comparable to manual counts of the aerial photographs by an expert (<5% difference). The procedure does not need any supervision of the extraction by an operator, thus reducing the processing time required to get the estimate of bird numbers in the image from >4 h to 20 min on average. Conclusion This open-source freeware should be useful for ornithologists and wildlife managers.