BackgroundIt　is　becoming　increasingly　clear　that　the　quantification　of　mitochondria　and　synapses　is　of　great　significance　to　understand　the　function　of　biological　nervous　systems.　Electron　microscopy　(EM),　with　the　necessary　resolution　in　three　directions,　is　the　only　available　imaging　method　to　look　closely　into　these　issues.　Therefore,　estimating　the　number　of　mitochondria　and　synapses　from　the　serial　EM　images　is　coming　into　prominence.　Since　previous　studies　have　achieved　preferable　2D　segmentation　performance,　it　holds　great　promise　to　obtain　the　3D　connection　relationship　from　the　2D　segmentation　results.ResultsIn　this　paper,　we　improve　upon　Matlab＇s　function　bwconncomp　and　propose　a　fast　forward　3D　connection　algorithm　for　mitochondria　and　synapse　segmentations　from　serial　EM　images.　To　benchmark　the　performance　of　the　proposed　method,　two　EM　datasets　with　the　annotated　ground　truth　are　produced　for　mitochondria　and　synapses,　respectively.　Experimental　results　show　that　the　proposed　method　can　achieve　the　preferable　connection　performance　that　closely　matches　the　ground　truth.　Moreover,　it　greatly　reduces　the　computational　burden　and　alleviates　the　memory　requirements　compared　with　the　function　bwconncomp.ConclusionsThe　proposed　method　can　be　deemed　as　an　effective　strategy　to　obtain　the　3D　connection　relationship　from　serial　mitochondria　and　synapse　segmentations.　It　is　helpful　to　accurately　and　quickly　quantify　the　statistics　of　the　numbers,　volumes,　surface　areas,　and　lengths,　which　will　greatly　facilitate　the　data　analysis　of　neurobiology　research.