Automatic Fish Counting in Aquariums Electrical and Computer Engineering

75 Pages·2016·4.76 MB·English

by  Andre C. Marta

Automatic Fish Counting in Aquariums
Francisco João Lourenço Silvério
Thesis to obtain the Master of Science Degree in
Electrical and Computer Engineering
Supervisor(s): Prof. João Nuno de Oliveira e Silva
Dr. José Almeida Cruz
Examination Committee
Chairperson: Prof. Nuno Cavaco Gomes Horta
Supervisor(s): Prof. João Nuno de Oliveira e Silva
Member of the Committee: Prof. Paulo Luis Serras Lobato Correia
May 2016
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TotheonesIlove
“Thisisnottheend,Noteventhe
beginningoftheend,Buttheend
ofthebeginning.”
-SirWinstonChurchill
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Acknowledgments
IwouldfirstliketoexpressmydeepgratitudetoChampalimaudFoundationCentrefortheUnknownfor
havinggivenmetheopportunityofdevelopingsuchaninterestingandmotivatingproject.
Also,Iwouldliketotakethischancetodemonstratemymostsinceregratitudeanddeepconsidera-
tiontomyextremelydedicatedsupervisors. ProfessorJoa˜oNunoSilvawhowasessentialinaccepting
me as a Master student of his, for enlightening me with his precious insights, guidance and always act
in my best interest. Dr. Jose´ Cruz, who was crucial in guaranteeing the cooperation with Champali-
maudFoundation,forhisextremelyimportanttechnicalinputsinthisprojectaswellashisavailabilityto
discussanydifficultiesthateventuallycameup.
AnaCatarinaCertal,JoanaMonteiroandallthestaffattheChampalimaudFoundationFishFacility
fortheirconstantavailabilityandcooperationinvideorecordingofthefish.
Ricardo Ribeiro, Carlos Ma˜o-de-Ferro and Alexandre Laborde, who I now consider as friends, for
beingsosupportiveandcooperativeduringmycollaborationattheNeurosciences’SoftwarePlatform.
AnotherspecialwordofthankfulnessdirectedtothefriendsIhadthepossibilitytomakeatInstituto
SuperiorTe´cnico. Idothoroughlybelievethatallthosememorablemomentsandadventuresweshared
willneverperishintime. Amongthesefriends,thereareuniquepeoplewhodeserveaspecialmention
for the deep friendship. Miguel Cirne with who I had the privilege to meet at the very beginning of
mypresenceatInstitutoSuperiorTe´cnicoandworkinextremelydemandingprojectsinwhichwecould
alwayssucceedwithdeepcommitmentanddedication. Ididalsohavetheopportunitytoknowandwork
with Miguel Fernandes with who I fought so many difficult battles throughout our engineering degree.
Thethreeofuscouldlearnandgrowtogetherasengineersbut,aboveall,aspersonsandIbelievethat
thisfriendshipwilllast.
Itakethisopportunitytoexpressmymostdeepestgratitudetomyspecialone,AnaFerreira. Words
arenotenoughtodescribehowspecialandimportantshewasduringmydegree,givingmehersupport,
patience,unconditionalloveandbydemonstratingherextremebeliefinmewhenIneededitthemost.
Finally, I conclude with a few words for my family. First I would like to express my gratitude to my
brother Joa˜o for representing an example for me of the engineer I would like to be one day, for the
technicalhelphecouldprovidemeduringthepastyearsandforbeingthereformeasanolderbrother.
To my sister Joana, who always stood beside me as a second mother from the very beginning of my
academic path and for the constant encouragement and motivation she could always transmit to me.
Por u´ltimo escrevo umas palavras para a minha ma˜e, Irene assim como para o meu pai, Fernando.
E´ aos meus pais que devo tudo aquilo que consegui alcanc¸ar ate´ hoje tanto a n´ıvel pessoal como
profissional. Semoseuapoio,incentivo,exemplo,sacrif´ıcio,plenaconfianc¸anasminhascapacidadese
asuapreocupac¸a˜oconstantecomaminhaeducac¸a˜o,na˜oteriasidoposs´ıvelconcluirestata˜ohe´rculea
etapa. E´ destaforma,agradecendoecomorgulho,quelhesdedicoestadissertac¸a˜o. Obrigado.
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Resumo
Fishfacilitiesportodoomundorecorremapeixeszebra(zebrafish)paraefectuarexperieˆncias. Aolongo
da sua vida, os peixes zebra sa˜o mantidos em aqua´rios e necessitam de ser contados, manualmente,
oqueconstituiumatarefamorosaequeesta´ sujeitaaerros.
Estetrabalhoapresentaumsistemaautoma´ticodecontagemdepeixeseumalgoritmobaseadoem
visa˜ocomputacionalpararealizaratarefa. Oalgoritmoutilizate´cnicasstandarddevisa˜ocomputacional
como subtrac¸a˜o de fundo, isolamento de blobs e compensac¸a˜o de reflexo˜es de forma a realizar uma
contagem mais precisa. Dado que as fish facilities teˆm mu´ltiplas categorias de peixes, o algoritmo
propostofoicalibradoparagarantirosmelhoresresultadosparamaisdoqueumacategoria.
Esteprojectoincluitambe´modesign,desenvolvimentoeimplementac¸a˜odeumsistemadehardware
completocomoobjectivodeadquirirvideosdepeixesdentrodeaqua´rios. Experieˆnciasrealizadasem
amostrasdevideoreaisdemonstramqueoalgoritmopropostoestimacomsucessoonu´merodepeixes
num tanque com uma margem de erro de aproximadamente 15% do nu´mero real. Relativamente ao
tempodeexecuc¸a˜odoalgoritmo,concluiu-sequeotemponecessa´rioparaestimaronu´merodepeixes
e´,emgeral,inferioraotempoquete´cnicosespecializadosdemoramarealizarumacontagemmanual.
Como trabalho futuro, a identicac¸a˜o de diferentes tipos de feno´tipos assim como a contagem do
nu´merodemachoefeˆmeasemaqua´rios,sa˜oexemplosdeideiasinteressantesquepodemserimple-
mentadasnestetipodeaplicac¸o˜es.
Palavras-chave:
visa˜ocomputacional,contagemdepeixeszebra,subtrac¸a˜odefundo,opti-
calflow,momentosdeHu,processamentodeimagem
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Abstract
Fishfacilitiesaroundtheworldresorttozebrafishtoperformexperiments. Duringtheirlifetime,fishare
maintained in tanks and need to be manually counted representing a time consuming and error prone
task.
This work presents an automatic fish counting setup and a computer vision based algorithm to per-
form the task. The algorithm uses image processing methods such as background subtraction, blob
isolationandmirroringcompensationtoperformamoreprecisefishcounting.
Sincefishfacilitieshavemultiplecategoriesoffish,theproposedalgorithmwascalibratedtoguaran-
tee the best results for more than one category. Moreover, this project does also comprise the design,
developmentandimplementationofafullhardwaresetupforthevideorecordingoffishinsidetanks.
Experimentsonrealvideosamplesshowthattheproposedalgorithmcansuccessfullyestimatethe
numberoffishinatankwithanerrormarginbelow15%oftherealfishnumberinsideatank.
Regarding algorithm execution time, we could conclude that the time needed to output an estimate
ofthenumberoffishinatankislowerthanthemanualcountingperformedbytechnicians.
Infuturework, theidentificationofmultiplephenotypesaswellascountingthenumberofmaleand
femaleinsidetanks,areexamplesofveryinterestingideaswhichshouldbeimplementedinthistypeof
solution.
Keywords:
computer vision, zebrafish counting, background subtraction, optical flow, Hu mo-
ments,imageprocessing
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