text: Search.setIndex({docnames:["documentation","index","installation","manual","quickstart"],envversion:{"sphinx.domains.c":2,"sphinx.domains.changeset":1,"sphinx.domains.citation":1,"sphinx.domains.cpp":3,"sphinx.domains.index":1,"sphinx.domains.javascript":2,"sphinx.domains.math":2,"sphinx.domains.python":2,"sphinx.domains.rst":2,"sphinx.domains.std":1,sphinx:56},filenames:["documentation.rst","index.rst","installation.rst","manual.rst","quickstart.rst"],objects:{"caiman.analysis":{Analysis:[0,1,1,""]},"caiman.analysis.Analysis":{correct:[0,2,1,""],distplot:[0,2,1,""],get_gmm:[0,2,1,""]},"caiman.dataset":{Dataset:[0,1,1,""]},"caiman.dataset.Dataset":{get_xprs:[0,2,1,""]},"caiman.model":{CheckPoint:[0,1,1,""],Expectation:[0,1,1,""],GaussianMixtureModel:[0,1,1,""]},"caiman.model.CheckPoint":{iteration:[0,3,1,""],means:[0,3,1,""],num_augmented_components:[0,3,1,""],stds:[0,3,1,""],weights:[0,3,1,""]},"caiman.model.Expectation":{conditional:[0,3,1,""],log_likelihood:[0,3,1,""],posterior:[0,3,1,""]},"caiman.model.GaussianMixtureModel":{fit:[0,2,1,""],get_means:[0,2,1,""],get_num_components:[0,2,1,""],get_stds:[0,2,1,""],log_likelihood:[0,2,1,""],posterior:[0,2,1,""],predict:[0,2,1,""],sample:[0,2,1,""]},"caiman.utils":{augment_data:[0,4,1,""],get_random_state:[0,4,1,""],have_same_index:[0,4,1,""],is_1darray:[0,4,1,""],is_file:[0,4,1,""],is_integer:[0,4,1,""],is_positive_integer:[0,4,1,""],is_series_dataframe:[0,4,1,""],likelihood_ratio_test:[0,4,1,""],read_series:[0,4,1,""],reduce_data:[0,4,1,""]},caiman:{analysis:[0,0,0,"-"],dataset:[0,0,0,"-"],model:[0,0,0,"-"],utils:[0,0,0,"-"]}},objnames:{"0":["py","module","Python module"],"1":["py","class","Python class"],"2":["py","method","Python method"],"3":["py","attribute","Python attribute"],"4":["py","function","Python function"]},objtypes:{"0":"py:module","1":"py:class","2":"py:method","3":"py:attribute","4":"py:function"},terms:{"000":2,"0000000e":3,"0063429e":3,"04356705":3,"06010501":3,"07132469":3,"09662524":3,"100":3,"1000":3,"10474598":3,"1080":0,"125":0,"17445941":3,"1948496e":3,"2125125":3,"2131582e":3,"2536421e":3,"2637395e":3,"3093626e":3,"36919074":3,"3778638e":3,"4108940e":3,"4817781e":3,"51180642":3,"5182225e":3,"543127":3,"5891063e":3,"590845":3,"5966247":3,"6074827e":3,"6221364e":3,"6906377e":3,"720":0,"73190427":3,"7362605e":3,"7392517e":3,"7463582e":3,"7868416e":3,"8051498e":3,"81309644":3,"9015721e":3,"94915712":3,"9936570e":3,"class":0,"default":[0,2,4],"float":0,"function":0,"import":3,"int":0,"log\u2082":1,"return":[0,3],"true":[0,3],"while":[3,4],For:[1,3],The:[0,1,2,3,4],There:4,These:1,__main__:[],across:[0,1],activ:2,adapt:[1,4],adaptive_num_compon:[0,3],add:[0,2],addit:0,adjust:[1,4],adpative_num_compon:3,affect:1,after:[1,2,3,4],aim:[],algorithm:[0,1,4],all:[0,4],also:[3,4],analysi:[1,2,3],analysis_requir:2,ani:[0,1,4],api:3,applic:3,approxim:1,argument:4,arrai:3,associ:1,attribut:[0,3],augment:[0,1],augment_data:0,augmet:0,avail:1,axi:0,base:[0,1],bash:[],been:[0,1],befor:0,being:[],believ:1,belong:0,between:1,bin:0,bind:[],bioconda:2,bioinformatician:3,block:[],bokeh:2,bool:0,bug:1,caiman:[2,3,4],caiman_out:[3,4],caiman_output:4,can:[0,2,4],cannot:0,cell:1,center:[0,1],channel:2,check:0,checkpoint:0,clone:2,close:[],code:2,column:[0,4],com:2,come:[],command:[2,4],complet:4,complex:0,compon:[0,1,3,4],comput:0,concaten:1,concept:[],conda:2,condit:0,config:2,consist:4,consortium:2,contain:[0,2,4],control:3,copi:0,core:[0,4],correct:[0,1,4],correspond:[0,4],count:[1,4],cpu:0,creat:2,custom:0,data:[0,1,4],datafram:0,dataset:[1,3,4],deep:0,defin:1,defualt:0,degre:0,denot:3,design:1,determin:[0,4],develop:[1,3],deviat:[0,1,3],dict:0,dictionari:0,dimension:0,directli:4,directori:[0,2,4],discoveri:[],dist:4,distplot:[0,3],distribut:[0,1,4],dn070017:[],doc:[],document:1,doe:0,download:[2,4],downstream:1,drawn:0,dtype:3,due:[],dure:0,each:[0,2,3,4],either:4,elaps:0,element:[0,3],embryon:3,enabl:[0,4],encod:2,environ:1,equal:1,error:0,estim:0,event:0,everi:[0,3],exampl:1,execut:[3,4],exist:0,exit:4,expect:0,express:[0,1,2,4],extract:0,facial:3,fals:[0,1,3],feedback:1,figur:[0,1],figure_s:0,file:[0,2,4],filter:[0,1,3,4],first:[0,3,4],fit:[0,1,4],fix:1,float32:[0,3],follow:[0,1,2,4],forc:0,forebrain:3,forg:2,form:1,format:[0,4],found:[2,4],frame:0,freedom:0,from:[0,1,2],gaussian:[0,1],gaussianmixturemodel:[0,1,4],gene:[0,1,2,4],gener:0,get:[0,3,4],get_gmm:[0,3],get_mean:[0,3],get_num_compon:0,get_random_st:0,get_std:[0,3],get_xpr:0,git:2,github:[1,2],given:[0,3],gmm:[0,3,4],group:[0,2,3,4],half:0,has:0,have:[0,1,4],have_same_index:0,header:[0,4],heart:3,height:0,help:4,high:1,highli:2,hindbrain:3,histogram:0,how:1,html:[0,4],http:[],identifi:[],illustr:0,improv:1,includ:2,increas:[],index:[0,1],index_col:3,inform:[0,1,2,4],inplac:[],input:[0,1],inspir:[],instal:[1,4],instanc:[0,4],integ:0,interact:[0,1,4],interfac:3,intestin:3,introduc:1,is_1darrai:0,is_aug:0,is_fil:0,is_fit:[0,3],is_integ:0,is_positive_integ:0,is_series_datafram:0,iter:0,karg:0,kidnei:3,kuijjer:1,kuijjerlab:2,lab:1,label:[0,3],later:[],lead:1,level:[1,4],like:4,likelihood:[0,4],likelihood_ratio_test:0,limb:3,linspac:3,list:[0,4],liver:3,load:0,log2:0,log:0,log_likelihood:0,log_likelihood_complex:0,log_likelihood_simplif:0,log_likelihood_simplifi:0,loglikelihood:0,lowli:1,lung:3,mai:1,mainli:[],make:[0,1],manual:1,manuscript:[1,2],manuscript_analysi:4,max_iter:0,maxim:0,maximum:0,mean:[0,1,3],memori:0,messag:[0,4],method:[0,2,3,4],midbrain:3,might:1,mixnorm:[],mixtur:[0,1],model:[1,3,4],modifi:[],modul:4,monitor:0,more:3,moreov:0,mous:2,mtrand:0,must:[0,4],name:[0,4],ndarrai:0,neg:1,network:1,neural:3,nois:[0,1,4],non:[0,1],none:0,normal:[0,1,4],note:4,num_augmented_compon:0,num_compon:3,num_flank_compon:0,num_gen:0,num_group:0,num_iter:3,num_sampl:0,number:[0,4],numpi:0,object:0,observ:[],off:[],one:[0,4],onli:0,optim:[0,4],option:[0,4],order:0,origin:0,other:[],outdir:[0,3,4],output:[0,4],overview:1,pacakg:[],packag:1,page:1,panda:0,paramet:[0,3],pass:0,path:[0,3,4],peak:0,pip:2,pipelin:[],pixel:0,pleas:[0,1,3],portion:0,posit:[0,1,4],possibl:0,posterior:[0,1,4],predict:[0,1],preprocess:4,print:3,probabl:[0,1,4],process:[0,1],profil:0,program:3,project:2,promin:3,propos:[],provid:[0,2,3,4],pvalu:0,python3:[],python:[1,2,3,4],qsmooth:4,quantil:1,quick:1,rais:0,random:0,randomli:[0,2],randomst:0,rate:[],ratio:[0,4],read:[0,4],read_csv:0,read_seri:0,realpath:3,recommend:2,reduc:0,reduce_data:0,refer:0,regardless:0,remain:[],remov:1,replac:[0,1],report:1,repres:[0,4],reproduc:[1,2],requir:0,respect:1,result:[0,3,4],rna:1,row:[0,4],run:0,same:0,sampl:[0,1,2,4],save:4,save_model:4,search:[],second:[0,3,4],see:1,seed:0,select:[1,2],self:0,sep:3,separ:[0,4],seq:1,seri:0,set:1,shape:[],share:0,should:[0,4],show:4,simplifi:0,size:0,smooth:1,snakemak:4,softwar:1,some:[],sourc:[0,2],source_nam:0,specif:[1,3],specifi:0,standard:[0,1,3],start:1,state:0,statist:1,std:[0,3],stomach:3,store:0,store_checkpoint:[0,3],str:0,strongli:[],structur:0,subdirectori:4,symmetr:1,system:0,tab:[0,4],tabl:[0,4],take:4,target:0,target_nam:0,test:[0,2,3,4],thereaft:1,therefor:[],thi:[0,1,2,3,4],those:1,threshold:1,time:0,timestamp:0,tissu:2,tmp:0,to_csv:3,took:[],transform:1,transpos:0,treat:4,tsv:[2,3,4],tube:3,tupl:[0,3],turn:[],two:[0,4],txt:2,under:2,union:0,uniqu:0,univari:0,unmodifi:[],unset:4,updat:0,usag:[0,4],use:[0,2,4],used:[0,1,3,4],user:[0,2],uses:[],using:[0,2,4],util:1,valu:[0,3],variabl:[0,1],vector:0,verbos:[0,3,4],virtual:2,visual:[0,1,4],want:[0,3],warn:0,weight:0,when:4,whether:[0,4],which:1,who:3,width:0,within:[],without:[0,4],work:1,x_limit:0,xpr:[0,3,4],yield:[],zero:[0,1]},titles:["Documentation","Caiman","Installation","Manual","Quick Start"],titleterms:{analysi:[0,4],caiman:[0,1],conent:[],content:1,correct:3,data:3,dataset:[0,2],doc:[],document:0,environ:2,exampl:2,express:3,fit:3,from:3,gaussianmixturemodel:3,get:[],indic:[],inform:3,input:3,instal:2,interact:3,introduct:1,issu:1,manual:3,manuscript:4,method:1,model:0,packag:2,posterior:3,predict:3,probabl:3,quick:4,reproduc:4,sampl:3,set:2,start:4,statist:3,tabl:1,util:0,visual:3}})