Automatic multiple zebrafish tracking based on improved HOG features

Scientific Reports
Yun-Xiang BaiMingzhu Sun

Abstract

As an excellent model organism, zebrafish have been widely applied in many fields. The accurate identification and tracking of individuals are crucial for zebrafish shoaling behaviour analysis. However, multi-zebrafish tracking still faces many challenges. It is difficult to keep identified for a long time due to fish overlapping caused by the crossings. Here we proposed an improved Histogram of Oriented Gradient (HOG) algorithm to calculate the stable back texture feature map of zebrafish, then tracked multi-zebrafish in a fully automated fashion with low sample size, high tracking accuracy and wide applicability. The performance of the tracking algorithm was evaluated in 11 videos with different numbers and different sizes of zebrafish. In the Right-tailed hypothesis test of Wilcoxon, our method performed better than idTracker, with significant higher tracking accuracy. Throughout the video of 16 zebrafish, the training sample of each fish had only 200-500 image samples, one-fifth of the idTracker's sample size. Furthermore, we applied the tracking algorithm to analyse the depression and hypoactivity behaviour of zebrafish shoaling. We achieved correct identification of depressed zebrafish among the fish shoal based on the ac...Continue Reading

References

Mar 17, 2011·PloS One·Jonathan CachatAllan V Kalueff
Feb 2, 2013·Science·Andrew BerdahlIain D Couzin
Mar 8, 2013·PLoS Computational Biology·Kolbjørn TunstrømIain D Couzin
Oct 3, 2015·Advances in Experimental Medicine and Biology·Kayo SugitaniSatoru Kato
Feb 18, 2017·Scientific Reports·Zhiping Xu, Xi En Cheng
Jul 1, 2017·PloS One·Zhi-Ming Qian, Yan Qiu Chen
Dec 16, 2017·Scientific Reports·Xiaoying WangDonald Wlodkowic

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Citations

Aug 16, 2019·Disease Models & Mechanisms·Yijie Geng, Randall T Peterson
Feb 7, 2021·Scientific Reports·Marta de Oliveira BarreirosAllan Kardec Barros
May 1, 2021·Scientific Reports·Marta de Oliveira BarreirosAllan Kardec Barros
Apr 27, 2021·Frontiers in Neuroscience·Nils OhnesorgeLars Lewejohann

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Methods Mentioned

BETA
Feature extracting

Software Mentioned

IdTracker
mathop
MATLAB

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