enable_job_accounting: bool = True,
enable_job_progress: bool = True,
enable_workflow_analytics: bool = True,
- sqlalchemy_url: str = None):
+ sqlalchemy_url: str = None,
+ config_only: bool = False):
"""
Initializes a new instance of the SlurmClient class.
@@ -524,18 +525,22 @@ Source code for biomero.slurm_client
self.get_or_create_github_session()
self.init_workflows()
- self.validate(validate_slurm_setup=init_slurm)
- # Setup workflow tracking and accounting
- # Initialize the analytics settings
- self.track_workflows = track_workflows
- self.enable_job_accounting = enable_job_accounting
- self.enable_job_progress = enable_job_progress
- self.enable_workflow_analytics = enable_workflow_analytics
+ if not config_only:
+ self.validate(validate_slurm_setup=init_slurm)
- # Initialize the analytics system
- self.sqlalchemy_url = sqlalchemy_url
- self.initialize_analytics_system(reset_tables=init_slurm)
+ # Setup workflow tracking and accounting
+ # Initialize the analytics settings
+ self.track_workflows = track_workflows
+ self.enable_job_accounting = enable_job_accounting
+ self.enable_job_progress = enable_job_progress
+ self.enable_workflow_analytics = enable_workflow_analytics
+
+ # Initialize the analytics system
+ self.sqlalchemy_url = sqlalchemy_url
+ self.initialize_analytics_system(reset_tables=init_slurm)
+ else:
+ logger.warning("Setup SlurmClient for config only")
[docs] def initialize_analytics_system(self, reset_tables=False):
"""
@@ -958,7 +963,8 @@ Source code for biomero.slurm_client
[docs] @classmethod
def from_config(cls, configfile: str = '',
- init_slurm: bool = False) -> 'SlurmClient':
+ init_slurm: bool = False,
+ config_only: bool = False) -> 'SlurmClient':
"""Creates a new SlurmClient object using the parameters read from a
configuration file (.ini).
@@ -1078,7 +1084,8 @@ Source code for biomero.slurm_client
enable_job_accounting=enable_job_accounting,
enable_job_progress=enable_job_progress,
enable_workflow_analytics=enable_workflow_analytics,
- sqlalchemy_url=sqlalchemy_url)
+ sqlalchemy_url=sqlalchemy_url,
+ config_only=config_only)
[docs] def cleanup_tmp_files(self,
slurm_job_id: str,
diff --git a/biomero.html b/biomero.html
index ff6888a..fda1fac 100644
--- a/biomero.html
+++ b/biomero.html
@@ -111,7 +111,7 @@ biomero packagebiomero.slurm_client module
-
-class biomero.slurm_client.SlurmClient(host='slurm', user=None, port=None, config=None, gateway=None, forward_agent=None, connect_timeout=None, connect_kwargs=None, inline_ssh_env=True, slurm_data_path: str = 'my-scratch/data', slurm_images_path: str = 'my-scratch/singularity_images/workflows', slurm_converters_path: str = 'my-scratch/singularity_images/converters', slurm_model_paths: Optional[dict] = None, slurm_model_repos: Optional[dict] = None, slurm_model_images: Optional[dict] = None, converter_images: Optional[dict] = None, slurm_model_jobs: Optional[dict] = None, slurm_model_jobs_params: Optional[dict] = None, slurm_script_path: str = 'slurm-scripts', slurm_script_repo: Optional[str] = None, init_slurm: bool = False, track_workflows: bool = True, enable_job_accounting: bool = True, enable_job_progress: bool = True, enable_workflow_analytics: bool = True, sqlalchemy_url: Optional[str] = None)[source]
+class biomero.slurm_client.SlurmClient(host='slurm', user=None, port=None, config=None, gateway=None, forward_agent=None, connect_timeout=None, connect_kwargs=None, inline_ssh_env=True, slurm_data_path: str = 'my-scratch/data', slurm_images_path: str = 'my-scratch/singularity_images/workflows', slurm_converters_path: str = 'my-scratch/singularity_images/converters', slurm_model_paths: Optional[dict] = None, slurm_model_repos: Optional[dict] = None, slurm_model_images: Optional[dict] = None, converter_images: Optional[dict] = None, slurm_model_jobs: Optional[dict] = None, slurm_model_jobs_params: Optional[dict] = None, slurm_script_path: str = 'slurm-scripts', slurm_script_repo: Optional[str] = None, init_slurm: bool = False, track_workflows: bool = True, enable_job_accounting: bool = True, enable_job_progress: bool = True, enable_workflow_analytics: bool = True, sqlalchemy_url: Optional[str] = None, config_only: bool = False)[source]
Bases: fabric.connection.Connection
A client for connecting to and interacting with a Slurm cluster over
SSH.
@@ -450,7 +450,7 @@ biomero package
-
-classmethod from_config(configfile: str = '', init_slurm: bool = False) biomero.slurm_client.SlurmClient[source]
+classmethod from_config(configfile: str = '', init_slurm: bool = False, config_only: bool = False) biomero.slurm_client.SlurmClient[source]
Creates a new SlurmClient object using the parameters read from a
configuration file (.ini).
diff --git a/searchindex.js b/searchindex.js
index 1e51250..8e0d393 100644
--- a/searchindex.js
+++ b/searchindex.js
@@ -1 +1 @@
-Search.setIndex({docnames:["biomero","index","modules","readme_link","tutorial_link"],envversion:{"sphinx.domains.c":2,"sphinx.domains.changeset":1,"sphinx.domains.citation":1,"sphinx.domains.cpp":5,"sphinx.domains.index":1,"sphinx.domains.javascript":2,"sphinx.domains.math":2,"sphinx.domains.python":3,"sphinx.domains.rst":2,"sphinx.domains.std":2,"sphinx.ext.intersphinx":1,"sphinx.ext.viewcode":1,sphinx:56},filenames:["biomero.rst","index.rst","modules.rst","readme_link.md","tutorial_link.md"],objects:{"biomero.slurm_client":[[0,1,1,"","SlurmClient"],[0,1,1,"","SlurmJob"]],"biomero.slurm_client.SlurmClient":[[0,2,1,"","bring_listener_uptodate"],[0,2,1,"","check_job_status"],[0,2,1,"","cleanup_tmp_files"],[0,2,1,"","convert_cytype_to_omtype"],[0,2,1,"","convert_url"],[0,2,1,"","copy_zip_locally"],[0,2,1,"","extract_data_location_from_log"],[0,2,1,"","extract_job_id"],[0,2,1,"","extract_parts_from_url"],[0,2,1,"","from_config"],[0,2,1,"","generate_slurm_job_for_workflow"],[0,2,1,"","get_active_job_progress"],[0,2,1,"","get_all_image_versions_and_data_files"],[0,2,1,"","get_cellpose_command"],[0,2,1,"","get_conversion_command"],[0,2,1,"","get_image_versions_and_data_files"],[0,2,1,"","get_job_status_command"],[0,2,1,"","get_jobs_info_command"],[0,2,1,"","get_listeners"],[0,2,1,"","get_logfile_from_slurm"],[0,2,1,"","get_or_create_github_session"],[0,2,1,"","get_recent_log_command"],[0,2,1,"","get_unzip_command"],[0,2,1,"","get_update_slurm_scripts_command"],[0,2,1,"","get_workflow_command"],[0,2,1,"","get_workflow_parameters"],[0,2,1,"","get_zip_command"],[0,2,1,"","init_workflows"],[0,2,1,"","initialize_analytics_system"],[0,2,1,"","list_active_jobs"],[0,2,1,"","list_all_jobs"],[0,2,1,"","list_available_converter_versions"],[0,2,1,"","list_completed_jobs"],[0,2,1,"","parse_docker_image_version"],[0,2,1,"","pull_descriptor_from_github"],[0,2,1,"","run_commands"],[0,2,1,"","run_commands_split_out"],[0,2,1,"","run_conversion_workflow_job"],[0,2,1,"","run_workflow"],[0,2,1,"","run_workflow_job"],[0,2,1,"","setup_container_images"],[0,2,1,"","setup_converters"],[0,2,1,"","setup_directories"],[0,2,1,"","setup_job_scripts"],[0,2,1,"","setup_listeners"],[0,2,1,"","setup_slurm"],[0,3,1,"","slurm_converters_path"],[0,3,1,"","slurm_data_path"],[0,3,1,"","slurm_images_path"],[0,3,1,"","slurm_model_images"],[0,3,1,"","slurm_model_paths"],[0,3,1,"","slurm_model_repos"],[0,3,1,"","slurm_script_path"],[0,3,1,"","slurm_script_repo"],[0,2,1,"","str_to_class"],[0,2,1,"","transfer_data"],[0,2,1,"","unpack_data"],[0,2,1,"","update_slurm_scripts"],[0,2,1,"","validate"],[0,2,1,"","workflow_params_to_envvars"],[0,2,1,"","workflow_params_to_subs"],[0,2,1,"","zip_data_on_slurm_server"]],"biomero.slurm_client.SlurmJob":[[0,3,1,"","SLURM_POLLING_INTERVAL"],[0,2,1,"","cleanup"],[0,2,1,"","completed"],[0,3,1,"","error_message"],[0,2,1,"","get_error"],[0,3,1,"","job_id"],[0,3,1,"","job_state"],[0,3,1,"","ok"],[0,3,1,"","progress"],[0,3,1,"","slurm_polling_interval"],[0,3,1,"","submit_result"],[0,3,1,"","task_id"],[0,2,1,"","wait_for_completion"],[0,3,1,"","wf_id"]],biomero:[[0,0,0,"-","slurm_client"]]},objnames:{"0":["py","module","Python module"],"1":["py","class","Python class"],"2":["py","method","Python method"],"3":["py","attribute","Python attribute"]},objtypes:{"0":"py:module","1":"py:class","2":"py:method","3":"py:attribute"},terms:{"0":[1,3],"00":[3,4],"001":4,"01":[0,4],"02":4,"03":4,"04":4,"05":3,"06":4,"08":[3,4],"09":3,"1":[0,1,3],"10":[0,3,4],"100":[3,4],"1000":3,"1006116864":4,"1006305280":4,"10802":4,"10gb":[3,4],"10x":3,"117":4,"12":4,"12345":0,"126":4,"12m":4,"13":4,"1336":4,"13t17":4,"15":[3,4],"15gb":[3,4],"16":4,"17":4,"172":4,"18":4,"18gb":4,"1g":[3,4],"2":[0,1,3],"2014":4,"2017":4,"2020":3,"2022":4,"2023":[0,4],"2024":4,"21":[3,4],"22":[3,4],"2215916":4,"2222":4,"224":3,"224x224":3,"2269097984":4,"23":4,"23t08":4,"23t09":4,"24":4,"25":[3,4],"256x256":4,"27":4,"28":4,"2a":4,"2aoamjs0":4,"2b":4,"2c":4,"3":[1,3],"30":[3,4],"300":4,"31":4,"3184":4,"32":[3,4],"33":4,"3358":4,"34":4,"3406":4,"3500":4,"36":4,"37":4,"3a":4,"3b":1,"3c":4,"3m":4,"4":[1,3],"40":4,"4064":4,"4080":4,"4096":4,"41":4,"42":4,"43":4,"44":4,"45":[3,4],"45min":3,"46":4,"4672820":4,"4784967680":4,"48":4,"4j":3,"4x":4,"5":[1,3],"50":3,"5120":4,"52":4,"54":4,"5gb":4,"6":[1,3],"60":3,"600":4,"64":3,"6817":4,"695":4,"7":[3,4],"700":4,"777":4,"7zip":[1,3],"8":[3,4],"9":[3,4],"900":4,"982536":4,"982720":4,"997":3,"case":[3,4],"class":[0,1],"default":[0,3,4],"do":[3,4],"export":3,"final":[0,4],"float":0,"function":[0,3,4],"import":[1,3],"int":0,"long":[3,4],"new":[0,1,4],"null":4,"public":[3,4],"return":[0,3,4],"short":[3,4],"static":4,"true":[0,3,4],"try":[0,1,3],"var":4,"while":[0,3,4],A:[0,3],And:[3,4],As:4,At:[3,4],But:[3,4],By:[3,4],For:[3,4],IS:4,IT:4,If:[0,3,4],In:[3,4],It:[0,3,4],NOT:4,No:4,ONE:3,Of:4,On:4,One:[0,4],Or:[3,4],THAT:4,That:4,The:[0,3,4],Then:[3,4],There:4,These:[0,3,4],To:[3,4],WITH:0,Will:[0,4],With:3,_:3,__:4,_______:4,_______________________________________:4,__init__:3,__main__:[3,4],__name__:[3,4],_aggreg:4,_cellexpans:4,_cp_mask:3,_cpmask:4,_default:0,_imag:4,_job:3,_job_:3,_job_cpu:4,_mask_c1:4,_out_sep:0,_repo:[3,4],abl:4,about:[0,4],abov:[3,4],accept:[0,4],access:[1,3],accomplish:3,accord:[0,3,4],account:[0,1,3],acct:4,action:4,activ:[0,4],actual:[3,4],ad:[0,3,4],adapt:4,add:1,addendum:1,addit:[0,3],addition:3,address:[0,4],adjust:4,admin:3,advanc:4,after:[0,3,4],afterward:[3,4],ag:4,again:[3,4],aggreg:4,algorithm:4,alia:[3,4],aliv:4,all:[0,3,4],allow:[3,4],along:4,alreadi:[0,3,4],also:[0,3,4],altern:0,alwai:[3,4],am:4,amc:4,amount:4,amsterdam:[3,4],an:[0,1,4],analysi:[1,4],analyt:0,analyz:4,ani:[0,3,4],annot:4,anoth:[3,4],anyon:4,anyth:4,anywai:[0,4],anywher:4,apach:4,api:4,app:4,appar:4,append:3,appli:[3,4],applic:4,approach:4,appropri:[0,4],apptain:[1,3],apt:4,ar:[0,3,4],archiv:0,arg:0,argument:[0,4],argv:[3,4],around:4,arrai:0,art:4,asctim:3,ask:[3,4],assign:4,associ:[0,3,4],assum:[0,3,4],astyp:4,attach:[3,4],attack:4,attempt:0,attribut:[0,3],aug:4,authent:[3,4],authorized_kei:4,autom:[3,4],automat:[0,3,4],avail:[0,3,4],azur:1,azureadmin:4,azureus:4,b:3,back:[3,4],base:[0,3,4],base_path:4,bash:4,bashrc:4,basic:3,basicconfig:3,batch:1,becam:4,becaus:[3,4],becom:4,been:[3,4],befor:[0,4],behavior:0,behaviour:4,being:[0,4],below:[0,3,4],benefici:3,best:3,better:[3,4],between:[0,3,4],bfimg:3,bi:1,biaflow:[3,4],biaflowsjob:[3,4],big:4,biggest:4,bimg:3,bin:[3,4],binari:4,bioformats2raw:3,bioimag:[1,4],biomerostorag:4,biomerowork:4,bit:4,bitbucket:3,bj:[3,4],blob:[0,4],blog:4,blosc:3,bonu:4,bool:[0,4],borrow:4,both:[3,4],boutiqu:3,box:4,branch:[0,3,4],brief:3,bring:4,bring_listener_uptod:0,browser:4,bsst265:4,bugfix:4,build:[0,3,4],builddir:4,built:[3,4],bump:4,button:4,c1:4,c2:4,cacert:4,calcul:1,call:[3,4],can:[0,3,4],cancel:0,candl:4,cannot:0,cat:4,caus:4,cc:4,cd:[0,3,4],cell:[0,3,4],cell_diamet:0,cellexpans:1,cellexpansion_job:4,cellexpansion_repo:4,cellnumgranul:4,cellpos:[0,1,3],cellpose_imag:4,cellpose_job:[3,4],cellpose_job_cpu:4,cellpose_job_gr:[3,4],cellpose_job_mem:[3,4],cellpose_job_tim:3,cellpose_mask:4,cellpose_repo:[3,4],cellpose_v1:4,cellposemask:4,cellprob_threshold:[3,4],cellprofil:[1,3],cellprofiler_job:4,cellprofiler_repo:4,cellprofiler_result:4,cellprofiler_spot:4,cellprofiler_spot_job:4,cellprofiler_spot_repo:4,cellprofiler_v1:4,cells_aggreg:4,cells_cellexpans:4,cellsgranuleslabel:4,cellsnucleilabel:4,cellular:[3,4],cellularimagingcf:3,centroid:4,certif:4,cetera:3,cf:4,challeng:4,chan:[3,4],chang:[3,4],channel:[0,3,4],chapter:[3,4],cheap:4,cheaper:4,check:[0,3,4],check_job_statu:0,checkout:4,chmod:4,choos:4,chosen:[3,4],chown:4,chunk:3,ci:4,class_nam:0,class_objseg:4,classmethod:0,clean:4,cleanup:0,cleanup_tmp_fil:0,cli:3,click:4,client:[0,1,3],clone:[0,3,4],close:4,closesess:4,cloud:[1,3],cluster:[0,3],cluster_kei:4,cmd:[3,4],cmdlist:0,code:[1,4],coffe:[3,4],color:4,column:[0,4],com:[0,3,4],combin:4,come:[3,4],comma:0,command:[0,3],commandlin:[3,4],comment:[3,4],commerci:4,commit:4,commmand:4,common:4,commonwl:3,commun:4,compat:3,complet:[0,4],compon:4,compos:4,comput:[3,4],concaten:0,concept:0,conf:4,config:[0,1,4],config_fil:0,config_omero_:3,config_omero_logging_level:3,config_omero_master_host:3,configfil:[0,3,4],configur:[0,3,4],congratul:[3,4],conn:0,connect:[0,3,4],connect_kwarg:0,connect_timeout:0,connectionlostexcept:4,consecut:0,consist:3,consol:[3,4],constant:4,constructor:0,contain:[0,1],container:3,container_nam:[3,4],content:[3,4],context:4,contextmanag:0,continu:4,contributor:4,control:4,conveni:3,convers:0,convert:[0,3,4],convert_cytype_to_omtyp:0,convert_job_arrai:4,convert_url:0,converter_imag:0,copi:[0,3,4],copy_zip_loc:[0,3],copyleft:4,copyright:4,core:[3,4],correct:4,correctli:[3,4],correspond:[0,3],cost:[3,4],could:[0,3,4],count:4,count_nonzero:4,cours:[3,4],cover:4,cow:4,cp:[3,4],cp_model:[0,3],cppipe:4,cpproj:4,cpu:[3,4],creat:[0,3],creating_bia_workflow_and_adding_to_biaflows_inst:4,creation:0,credenti:4,credit:4,creditcard:4,crop:3,crt:4,csv:4,ctld:4,ctrl:4,current:[0,3,4],custom:1,cv2:4,cwd:3,cyclecloud:4,cython:4,cytomin:[0,3,4],cytomine_:3,cytomine_host:4,cytomine_id_project:4,cytomine_id_softwar:4,cytomine_job:0,cytomine_private_kei:4,cytomine_public_kei:4,cytoplasm:4,cytyp:0,d:[0,3],da:4,daemon:4,danger:4,data:[0,1],data_loc:0,data_path:[0,3],databas:0,datadisk:3,datafil:4,datafram:4,dataset:[3,4],date:[3,4],db:1,dbd:4,dbformysql:4,dd:0,de:4,debug:[3,4],deepcel:[3,4],deepcell_job:4,deepcell_repo:4,def:4,defin:[3,4],definit:[0,4],deleg:4,delet:[3,4],demand:4,deni:4,depend:[0,3],depends_on:4,deploi:[3,4],deploy:4,depth:3,deriv:4,descend:0,describ:[3,4],descript:[3,4],descriptor:[0,1],desir:3,desktop:4,destin:4,destroi:4,detail:[3,4],detect:0,dev:[3,4],devel:3,develop:4,diamet:[0,3,4],dict:0,dictionari:0,did:4,didn:4,differ:[3,4],digicert:4,digicertglobalrootca:4,dimens:3,dir:[3,4],directli:[3,4],directori:[0,3,4],dirti:4,discuss:3,distinguish:0,distribut:4,dl:[0,4],dn:4,doc:4,docker:[0,1],dockerfil:3,dockerfile_slurmctld:4,dockerhub:[0,3],dockerhub_token:4,dockerhub_usernam:4,docstr:3,document:[0,4],doe:[0,4],doesn:[0,3,4],don:[3,4],done:[3,4],dot:4,down:[3,4],download:[0,3,4],drastic:4,drive:[3,4],drop:0,drwxr:4,drwxrwxr:4,ds:4,dtype:4,dunde:4,dure:0,dyn:4,dynam:4,e:[0,3],each:[0,3,4],earlier:3,easi:[3,4],easier:[3,4],easiest:[0,3,4],easili:4,eavesdrop:4,echo:[3,4],edit:4,editor:4,effect:4,effici:3,either:[0,3,4],elaps:4,els:[0,3],email:[0,3,4],embarrassingli:3,empti:[0,4],en:4,enabl:[0,3],enable_job_account:0,enable_job_progress:0,enable_workflow_analyt:0,encapsul:0,encount:0,encourag:[3,4],end:[0,3,4],end_tim:0,endtim:4,enforc:3,enhanc:4,enjoi:4,enough:[3,4],ensur:[0,3,4],enter:4,entri:[0,4],entrypoint:[3,4],env:[0,4],environ:[0,3,4],equal:3,equip:3,err_desc:3,error:[0,3,4],error_messag:0,escap:4,especi:[3,4],essenti:4,estim:4,et:3,etc:[0,3,4],etc_mung:4,etc_slurm:4,etric:4,euro:4,europ:4,even:[3,4],everi:[3,4],everybodi:4,ex:4,exampl:[0,3,4],excel:4,except:[0,4],exec:4,execut:[0,3,4],exercis:4,exist:[0,1,4],exit:[3,4],expect:[0,3,4],expens:[3,4],expire_tim:4,explain:4,explan:3,explicitli:3,explor:[3,4],expos:4,ext:4,extend:[0,3],extens:[0,4],extern:[3,4],extra:[1,3],extract:[0,1],extract_data_location_from_log:0,extract_job_id:0,extract_parts_from_url:0,ezomero:3,f:[0,3,4],fabric:[0,3,4],facil:3,fact:3,fail:[0,3,4],failur:0,fair:[1,3],fals:[0,4],faster:[3,4],favorit:4,featur:3,few:4,field:3,figur:3,fiji:3,file:[0,3],filenam:[0,3],filename_no_extens:3,filepath:4,fileserv:4,filetyp:0,fill:[0,4],filler:4,filter:[0,4],filter_filetyp:0,find:[0,3,4],fine:4,finish:3,fire:4,firewal:4,first:[0,3,4],fit:4,fix:[0,4],flag:[0,3,4],flexibl:[3,4],flexibleserv:4,fluorescens:4,folder:[0,3,4],folder_nam:0,folk:4,follow:[0,3,4],forc:0,force_upd:0,forget:4,form:[3,4],format:[0,3,4],forward:[3,4],forward_ag:0,found:[0,3,4],framework:3,free:[3,4],friendli:3,from:[0,1,3],from_cli:[3,4],from_config:[0,3,4],full:[0,4],fulli:4,fun:[3,4],funni:4,futur:[0,3,4],fw:4,g:[0,3,4],gain:4,gatewai:[0,4],gb:[3,4],gcloud:4,gcslurm:4,gener:[0,1,4],generate_job:[0,3],generate_slurm_job_for_workflow:0,get:[0,4],get_active_job_progress:0,get_all_image_versions_and_data_fil:[0,4],get_cellpose_command:0,get_conversion_command:0,get_error:0,get_image_versions_and_data_fil:0,get_job_status_command:0,get_jobs_info_command:0,get_listen:0,get_logfile_from_slurm:[0,3],get_or_create_github_sess:0,get_recent_log_command:0,get_unzip_command:0,get_update_slurm_scripts_command:0,get_workflow_command:0,get_workflow_paramet:0,get_zip_command:0,getenv:4,getinput:4,getlogg:4,ghpc:4,giant:4,gid:3,giovtorr:4,git:[0,3,4],github:[0,3],give:[0,3,4],given:[0,3,4],global:3,gnu:4,go:4,godlovedc:4,good:4,googl:1,gosu:4,got:4,gpu:[0,1,4],grab:[1,3],granuleslabel:4,granulesstat:4,granulesstatsincelllabel:4,granulesstatsnp:4,grayscal:3,gre:4,great:4,grei:3,grid:4,ground:3,group:4,groupadd:4,gt:4,gt_img:[3,4],gt_path:[3,4],gtfolder:[3,4],guid:[3,4],gz:4,ha:[0,3,4],had:4,half:4,hand:4,handl:[3,4],handout:4,hardcod:[3,4],hardwar:3,have:[0,3,4],headbash:4,header:0,headless:3,heard:4,hello:3,help:3,helper:4,here:[3,4],hh:[0,3],hidden:4,high:3,higher:3,highli:4,hoc:4,hold:4,home:[3,4],hope:4,hopefulli:[3,4],host:[0,3,4],hostnam:[3,4],hour:3,how:1,howev:[0,3,4],hpc:[3,4],hpcsmall:4,htc:4,html:[3,4],htop:4,http:[0,3,4],hub:4,human:4,i:[1,4],iap:4,ic:4,id:[0,3,4],id_rsa:[3,4],idea:4,ideal:4,identif:4,identityfil:4,idkei:4,idl:4,ignor:[3,4],ij:3,ij_min_threshold:3,ij_radiu:3,ijm:3,imag:[0,3],image_nam:0,image_path:3,image_tag:4,image_vers:[0,3],imageio:3,imagej:[3,4],imagej_job:4,imagej_repo:4,imcellscelllabel:4,imcellsgranuleslabel:4,img:3,implement:[0,3,4],improv:[3,4],imread:[3,4],imread_anydepth:4,imwrit:3,in_img:[3,4],in_path:[3,4],inbound:4,incl:3,includ:[0,3,4],incur:3,indefinit:3,index:[0,1],indic:0,individu:0,infinit:4,info:[0,3,4],infold:[3,4],inform:[0,3,4],ingredi:4,ingress:4,ini:[0,1,4],init:[3,4],init_environ:4,init_slurm:[0,3,4],init_workflow:0,initi:[0,4],initialis:4,initialize_analytics_system:0,initscript:4,inject:3,inline_ssh_env:0,innodb_lock_wait_timeout:4,input:[0,3,4],input_data:0,input_fold:3,input_url:0,insert:4,insid:4,insight:[3,4],instal:[1,3],instanc:[0,3,4],instanti:[0,4],instead:[0,3,4],insuffici:4,int16:4,integr:[3,4],interact:[0,3,4],interfac:3,intern:4,internet:4,interoper:4,interv:0,introduct:1,invest:4,invok:0,involv:0,io:[3,4],ip:4,is_2d:[3,4],iso:0,isol:3,issu:[0,3,4],its:[0,3,4],jar:3,java:3,job:[0,1,4],job_id:0,job_stat:0,job_templ:[0,3,4],jobid:[0,4],jobnam:4,jobscript:[3,4],join:[3,4],json:[0,1],jump:4,just:[3,4],keep:[3,4],kei:[0,3,4],keygen:4,keyword:0,kickstart:4,kind:4,know:4,knowledg:4,known:[0,4],known_host:3,kwarg:0,la:4,last:[0,4],later:[0,4],latest:[0,3,4],launch:[3,4],law:4,lead:4,learn:4,least:3,leav:4,left:[3,4],less:[3,4],let:4,lethal:3,level:3,levelnam:3,lib:3,libgeo:4,librari:[0,3,4],licens:[1,3],lightweight:4,like:[0,3,4],limit:[0,1,4],line:[0,3,4],linear:4,link:[0,4],linux:4,lisbon:4,list:[0,4],list_active_job:0,list_all_job:0,list_available_converter_vers:0,list_completed_job:0,listen:0,liter:[3,4],ll:4,load:[0,4],local:[0,1,3],local_path:0,local_tmp_storag:0,localhost:[3,4],localslurm:4,locat:[0,3,4],log:[0,1,4],log_fil:0,logfil:[0,3,4],logger:[0,4],logic:4,login:[3,4],logout:4,lolcow:4,longer:[3,4],look:[0,3,4],lose:3,lot:[3,4],lower:4,ls:4,lt:4,luckili:4,luik:4,m:[3,4],mac:4,machin:[0,3,4],macro:3,made:[3,4],mage:3,magic:4,mai:4,mail:[3,4],main:[3,4],mainli:[3,4],major:4,make:[3,4],man:4,manag:[0,1,3],mandatori:[3,4],manipul:4,manual:3,map:[0,4],mar:4,march:4,mask:[1,3],master:[0,3,4],match:[0,3,4],matter:4,max:[3,4],maximum:[0,3],maxshap:3,maxvm:4,mayb:[3,4],mconfig:4,md:4,me:4,mean:4,meant:4,measur:4,mechan:0,medium:3,mem:4,memori:3,mention:0,merchant:4,messag:[0,3,4],metadata:1,method:[0,3,4],metric:[3,4],microscopi:4,microsoft:1,middl:4,might:[0,3,4],min:[3,4],min_threshold:3,mine:4,minim:[3,4],minshap:3,minut:[3,4],miss:[3,4],mkdir:4,mlflow:3,mm:[0,3],mnt:3,mod_pipelin:4,mode:4,model:[0,3,4],model_path:3,modern:4,modifi:4,modul:[1,2,3,4],module_nam:0,moment:4,monei:4,monitor:[0,3],month:4,more:[0,3,4],most:[0,4],mount:[3,4],move:3,movi:4,ms:4,much:4,multipl:[0,1,4],mung:4,must:[0,4],my:[0,3,4],myjob:0,mysql:4,n:[0,4],name:[0,3,4],namespac:4,nasti:4,ndarrai:4,ndata:4,necessari:[0,3],need:[0,3,4],net:4,network:3,neubia:[3,4],newest:4,newli:4,next:[0,3,4],nextflow:4,nf:0,ngc:4,nice:[3,4],nicer:3,nj:3,nl:[3,4],nmc:4,no_npi:[3,4],node:[3,4],nodelist:4,nodenam:4,nologin:4,non:[3,4],none:[0,3],normal:4,note2:3,note:[0,3,4],noth:0,notif:0,now:[0,3,4],np:4,nsdynam:4,nuc:[3,4],nuc_channel:[0,3,4],nuclear:0,nuclei:[0,4],nucleilabel:4,nucleu:4,num:4,number:[0,4],numcel:4,o:[0,1,4],object:[0,3],oblig:4,occur:0,off:4,offer:3,offload:4,ok:[0,4],old:[0,4],older:4,om:3,omero:[0,1],omero_worker_nam:3,omeroconn:0,omeroinsight:4,omeroserv:3,omeroweb:4,omerowork:4,omit:[0,3],omput:4,onc:[3,4],one:[0,3,4],ones:[0,4],onli:[0,3],onlin:4,onto:4,oo:4,op:4,open:4,openssh:4,oper:[0,3,4],opt:[3,4],option:[0,1,3],orchestr:4,order:0,origin:[0,3,4],original_fil:4,os:[3,4],osc:3,oserror:0,other:[0,3,4],otherwis:[0,3,4],our:[3,4],out:[0,3],out_path:[3,4],outfold:[3,4],output:[0,3,4],outsid:4,over:[0,3,4],overal:3,overhead:[3,4],overlap:1,overrid:[3,4],overview:1,overwrit:[0,4],own:[1,4],ownership:4,p7zip:4,p:4,packag:[2,3],package_upgrad:4,page:4,paid:4,pair:[0,4],parallel:[3,4],param:[0,3],param_nam:4,paramet:[0,1],paramiko:0,pars:[0,4],parse_cellprofiler_paramet:4,parse_docker_image_vers:0,parsecpparam:4,part:[0,4],particularli:[0,4],partit:4,pass:0,password:4,passwordless:3,past:4,path:[0,3,4],pattern:0,pd:4,peer:4,pem:4,pend:0,peopl:4,per:[0,3,4],perform:[0,3,4],perhap:[0,3,4],permiss:4,pick:4,pickup:4,pin:3,pip:[3,4],pipelin:[1,3],pitfal:3,pixel:0,pla:4,pla_data:4,place:3,placehold:[0,4],plai:4,plate:4,platform:3,pleas:[3,4],plugin:[3,4],png:4,podman:[3,4],point:[3,4],poll:[0,3],port:[0,3,4],portal:4,posit:0,possibl:[3,4],potenti:3,power:4,ppa:4,practic:[3,4],predict:3,prefix:4,prepar:[3,4],prepare_data:[3,4],preprocess:3,prerequisit:1,present:0,press:4,pretrained_model:[3,4],pretti:4,previou:3,price:4,primit:3,print:[0,3,4],prioriti:4,privat:[3,4],prob:3,prob_thresh:3,prob_threshold:[0,3,4],probabl:[0,4],problem:3,problem_cl:[3,4],proceed:0,process:[0,3,4],processor:[3,4],profil:4,program:[3,4],programmat:3,progress:[0,3,4],project:4,promot:4,promptless:4,proper:4,properli:[0,4],properti:4,protein:4,protocol:4,provid:[0,3,4],pub:[3,4],pubkei:3,publish:3,pull:[0,3,4],pull_descriptor_from_github:0,pull_imag:4,purpos:[0,3,4],push:4,put:[3,4],pw:4,py:[0,1],pypi:3,pytest:3,python3:[3,4],python:[0,1,4],quantifi:4,queri:0,queue:4,quick:[3,4],quicker:4,quickstart:1,quit:4,r:[0,4],radiu:3,rais:[0,3],ran:4,rang:4,raw:[0,4],re:4,reach:[0,4],read:[0,3],readabl:4,reader:4,readi:4,readm:4,realli:4,realmemori:4,reason:4,rebuild:4,receiv:0,recent:[0,4],recogn:4,recommend:3,recreat:[0,4],reduc:4,refer:[0,3,4],referenc:3,refresh:[3,4],region:4,regionprops_t:4,registr:4,rel:4,relat:[0,3,4],releas:[3,4],remain:[0,4],remot:[0,3,4],remov:[0,4],renam:4,replac:[3,4],repo:[0,3,4],repositori:[0,3],repres:0,reproduc:[3,4],request:[3,4],requir:[0,1],reserv:4,reset_t:0,resiz:3,resourc:[3,4],respons:0,rest:4,restart:4,restrict:4,result:[0,3,4],retain:[0,4],retri:0,retriev:[0,3,4],return_cod:3,returncod:3,reus:4,review:3,rewrit:3,rewrot:4,rgb:3,rich:4,right:4,rm:[3,4],rocki:4,rockylinux:4,role:4,root:4,rootless:4,round:4,row:4,rs:0,rstring:4,rtype:4,rule:4,run:[0,1,3],run_command:0,run_commands_split_out:0,run_conversion_workflow_job:0,run_workflow:[0,4],run_workflow_job:0,runcmd:4,runner:[0,4],runscript:[3,4],runtim:3,rw:4,rwxr:4,s:[0,3,4],sacct:[0,4],sadli:4,safe:4,sai:[3,4],same:[0,3,4],satisfi:4,save:4,save_tif:[3,4],sbatch:[0,3,4],sbin:4,sc:3,scale:4,scenario:3,schedmd:3,schedul:[3,4],schema:[1,4],scheme:3,scp:[0,3,4],scratch:[0,4],screen:[3,4],script:[0,1],scroll:4,second:[0,4],secret:[3,4],section:[3,4],secur:4,see:[0,1,4],seem:4,segment:[3,4],select:[3,4],send:[0,3],sep:0,separ:[0,4],seriou:4,server:[0,3,4],servic:4,session:0,set:[0,1,3],setoutput:4,setup:[0,1,3],setup_container_imag:0,setup_convert:0,setup_directori:0,setup_job_script:0,setup_listen:0,setup_slurm:0,sever:[3,4],sftp:3,sh:[0,3,4],shakespear:4,shame:4,shape:3,share:[0,3,4],sharg:4,shell:[0,3,4],shenanigan:4,shorter:3,should:[1,3],shoulder:4,show:[3,4],shown:4,showtim:1,shutil:3,side:4,sif:[0,3,4],sign:4,similar:[0,4],simpl:[0,3,4],simpli:3,simplifi:[3,4],sinc:4,sing:4,singl:0,singular:[0,1,3],singularity_imag:[0,3,4],singularity_vers:4,size:4,sleep:4,slow:3,slurm:[0,1],slurm_cellpose_segment:3,slurm_client:[1,2],slurm_config:4,slurm_converters_path:0,slurm_data_path:[0,3,4],slurm_images_path:[0,3,4],slurm_job_id:0,slurm_jobdir:4,slurm_model_imag:0,slurm_model_job:0,slurm_model_jobs_param:0,slurm_model_path:0,slurm_model_repo:0,slurm_polling_interv:0,slurm_run_workflow_batch:4,slurm_script_path:[0,3,4],slurm_script_repo:[0,3,4],slurmclient:[0,1,4],slurmctld:4,slurmdbd:4,slurmjob:0,small:4,smaller:[3,4],smart:[3,4],snakemak:4,so:[3,4],softwar:[3,4],solut:4,some:[0,3,4],someon:4,someth:[3,4],sort:0,sound:4,sourc:[0,3,4],source_format:0,south:4,space:[0,4],specif:[0,3,4],specifi:[0,3],speckl:4,speed:[3,4],speedup:4,spent:4,spin:[3,4],split:[0,4],spot:4,spotcount:4,spun:4,sqlalchemy_url:0,squeue:4,ss:[0,3],ssh:[0,1],sshd:4,sshdocker:4,sshexcept:0,sshgroup:4,sshuser:4,ssl:4,st:4,stai:[3,4],stain:4,stand:4,standard:3,standard_dc2s_v3:4,standard_dc4s_v3:4,standard_nd96amsr_a100_v4:4,stardist:[3,4],stardist_job:4,stardist_repo:4,start:[0,4],start_tim:0,starttim:4,state:[0,4],statu:[0,3,4],statuscom:[3,4],stdout:[0,3,4],step:[3,4],stick:4,still:[0,4],storag:[0,4],storageaccount:4,store:[0,3,4],str:[0,4],str_to_class:0,stream:3,stricthostkeycheck:4,strictli:3,string:[0,3,4],strong:3,strongli:4,stuff:4,style:4,sub:0,subdirectori:4,subfold:[0,4],subject:4,submiss:[0,3,4],submit:[0,3,4],submit_result:0,submitit:3,subprocess:[3,4],subscript:4,substitut:0,succeed:0,success:[0,4],successfulli:0,sudo:4,suffix:4,suit:4,superus:4,suppli:4,support:[0,3,4],sure:[3,4],sweet:4,sy:3,system:[0,4],systemctld:4,t:[0,3,4],t_nucleisegment:4,t_t_luik:4,t_t_luik_amsterdamumc_nl:4,tab:[3,4],tabl:4,tag:[0,3,4],tail:[3,4],take:[0,3,4],tar:4,target:[0,3],target_format:0,task:[0,3,4],task_id:0,tbc:3,tcp:4,tell:4,templat:[0,3,4],temporari:[0,4],term:4,termin:[3,4],test:1,testproject:4,text:[3,4],than:[3,4],thei:[3,4],them:[0,3,4],themselv:[0,4],theoret:3,theori:[3,4],thi:[0,1,3],thing:4,think:[3,4],third:4,those:[0,3,4],though:4,thought:1,threshold:[0,3,4],through:[3,4],thrown:4,tick:4,tif:[0,3,4],tiff:[0,3,4],tifffil:3,time:[0,1,4],timelimit:4,timeout:[0,3],tischi:4,tmp:[0,3],tmp_path:[3,4],to_numpi:4,togeth:[3,4],token:4,too:1,took:4,tool:0,top:4,torec:4,torecluik:[3,4],total:4,touch:4,toward:3,track:[0,4],track_workflow:0,trailer:0,transfer:[0,1],transfer_data:[0,3],transferresult:0,tree:[3,4],trick:4,troubl:4,trust:[3,4],truth:3,truthi:0,tue:4,tune:4,tupl:0,turn:[3,4],twice:4,two:0,txt:[3,4],type:[0,4],u:4,ubuntu:4,ui:[1,3],uid:3,uint16:4,uk:4,ulieg:[0,4],umc:[3,4],uncheck:[3,4],under:[3,4],understand:4,uniform:3,uniqu:[0,3,4],univers:4,unknown:4,unless:[3,4],unlik:0,unpack:[0,3],unpack_data:[0,3],until:[0,3],unvers:0,unwrap:4,unzip:[0,3],up:[0,1,3],updat:[0,3],update_slurm_script:[0,3],upgrad:4,upload:[1,3],url:[0,4],us:[0,1],use_gpu:[0,3,4],user:[0,3,4],useradd:4,userknownhostsfil:4,usern:3,usernam:[3,4],usr:[3,4],utf:4,util:[3,4],util_script:4,uuid:0,v0:4,v1:[3,4],v2:4,v3:4,v:4,valid:[0,3,4],validate_slurm_setup:[0,3,4],valu:[0,3,4],valueerror:[0,3],var_log_slurm:4,variabl:[0,3,4],variou:3,ve:4,venic:4,venv:[3,4],venvtest:3,veri:[3,4],verifi:4,version:[0,1,4],vi:4,via:[0,1,4],video:4,view:[0,4],vm:4,vnet:4,volum:[3,4],vs:4,w:[3,4],w_cellexpans:4,w_cellexpansion_v2:4,w_countmaskoverlap:4,w_countmaskoverlap_v1:4,w_nucleisegment:[3,4],w_spotcount:4,wa:[0,4],wai:[0,3,4],wait:[0,3,4],wait_for_complet:0,walk:4,want:[3,4],warn:[0,3,4],watch:3,we:[0,1,3],web:[1,3],websit:[3,4],wed:4,well:[3,4],were:4,western:4,wf:4,wf_id:0,wg5:4,wget:4,what:[0,3,4],whatev:4,when:[0,3,4],whenev:4,where:[0,3,4],whether:0,which:[0,3,4],whole:4,william:4,window:[3,4],within:[0,3,4],without:[0,4],won:4,work:[0,3,4],worker:4,workflow:[0,1],workflow_nam:0,workflow_params_to_envvar:0,workflow_params_to_sub:0,workflow_vers:0,workload:[0,4],world:3,worth:0,would:[3,4],wq:4,wrap:[3,4],wrapper:1,write:[3,4],wrong:4,wrote:4,x:[0,4],xmx6000m:3,xr:4,xvfb:3,xzf:4,y:[3,4],ye:4,yet:[0,3,4],yml:[0,3,4],you:[0,3,4],your:[0,1],yourself:3,yum:[3,4],yyyi:0,zarr:[0,3],zero:4,zip:[0,3,4],zip_data_on_slurm_serv:[0,3],zipfil:[0,4]},titles:["biomero package","Welcome to BIOMERO\u2019s documentation!","biomero","BIOMERO - BioImage analysis in OMERO","Cellprofiler tutorial"],titleterms:{"0":4,"1":4,"2":4,"3":4,"3b":4,"4":4,"5":4,"6":4,"7zip":4,"class":3,"export":4,"import":4,"new":3,"try":4,A:4,access:4,account:4,add:[3,4],addendum:4,altern:4,an:3,analysi:3,apptain:4,azur:4,b:4,basic:4,batch:[3,4],bi:4,bioimag:3,biomero:[0,1,2,3,4],c:4,calcul:4,cellexpans:4,cellpos:4,cellprofil:4,client:4,cloud:4,cluster:4,code:3,command:4,config:3,contain:[3,4],creat:4,custom:3,d:4,data:[3,4],databas:4,db:4,descriptor:[3,4],docker:[3,4],dockerfil:4,dockerhub:4,document:1,dr:4,e:4,exist:3,extra:4,extract:4,fair:4,file:4,from:4,gener:3,get:[1,3],github:4,googl:4,gpu:3,grab:4,headless:4,how:[3,4],i:3,imag:4,indic:1,ini:3,instal:4,introduct:4,job:3,json:[3,4],licens:4,limit:3,local:4,log:3,manag:4,manual:4,mask:4,memori:4,metadata:[3,4],microsoft:4,modul:0,multipl:3,network:4,o:3,omero:[3,4],onli:4,option:4,out:4,overlap:4,overview:3,own:3,packag:[0,1,4],paramet:[3,4],pipelin:4,prerequisit:[3,4],publish:4,py:[3,4],python:3,quickstart:3,repositori:4,requir:[3,4],run:4,s:1,schema:3,script:[3,4],see:3,set:4,setup:4,should:4,showtim:4,singular:4,slurm:[3,4],slurm_client:0,slurmclient:3,ssh:[3,4],start:[1,3],subnet:4,suggest:4,tabl:1,test:[3,4],thi:4,thought:4,time:3,tl:4,too:4,transfer:3,tutori:[1,3,4],ui:4,up:4,updat:4,upload:4,us:[3,4],version:3,via:3,virtual:4,we:4,web:4,welcom:1,workflow:[3,4],wrapper:[3,4],your:[3,4]}})
\ No newline at end of file
+Search.setIndex({docnames:["biomero","index","modules","readme_link","tutorial_link"],envversion:{"sphinx.domains.c":2,"sphinx.domains.changeset":1,"sphinx.domains.citation":1,"sphinx.domains.cpp":5,"sphinx.domains.index":1,"sphinx.domains.javascript":2,"sphinx.domains.math":2,"sphinx.domains.python":3,"sphinx.domains.rst":2,"sphinx.domains.std":2,"sphinx.ext.intersphinx":1,"sphinx.ext.viewcode":1,sphinx:56},filenames:["biomero.rst","index.rst","modules.rst","readme_link.md","tutorial_link.md"],objects:{"biomero.slurm_client":[[0,1,1,"","SlurmClient"],[0,1,1,"","SlurmJob"]],"biomero.slurm_client.SlurmClient":[[0,2,1,"","bring_listener_uptodate"],[0,2,1,"","check_job_status"],[0,2,1,"","cleanup_tmp_files"],[0,2,1,"","convert_cytype_to_omtype"],[0,2,1,"","convert_url"],[0,2,1,"","copy_zip_locally"],[0,2,1,"","extract_data_location_from_log"],[0,2,1,"","extract_job_id"],[0,2,1,"","extract_parts_from_url"],[0,2,1,"","from_config"],[0,2,1,"","generate_slurm_job_for_workflow"],[0,2,1,"","get_active_job_progress"],[0,2,1,"","get_all_image_versions_and_data_files"],[0,2,1,"","get_cellpose_command"],[0,2,1,"","get_conversion_command"],[0,2,1,"","get_image_versions_and_data_files"],[0,2,1,"","get_job_status_command"],[0,2,1,"","get_jobs_info_command"],[0,2,1,"","get_listeners"],[0,2,1,"","get_logfile_from_slurm"],[0,2,1,"","get_or_create_github_session"],[0,2,1,"","get_recent_log_command"],[0,2,1,"","get_unzip_command"],[0,2,1,"","get_update_slurm_scripts_command"],[0,2,1,"","get_workflow_command"],[0,2,1,"","get_workflow_parameters"],[0,2,1,"","get_zip_command"],[0,2,1,"","init_workflows"],[0,2,1,"","initialize_analytics_system"],[0,2,1,"","list_active_jobs"],[0,2,1,"","list_all_jobs"],[0,2,1,"","list_available_converter_versions"],[0,2,1,"","list_completed_jobs"],[0,2,1,"","parse_docker_image_version"],[0,2,1,"","pull_descriptor_from_github"],[0,2,1,"","run_commands"],[0,2,1,"","run_commands_split_out"],[0,2,1,"","run_conversion_workflow_job"],[0,2,1,"","run_workflow"],[0,2,1,"","run_workflow_job"],[0,2,1,"","setup_container_images"],[0,2,1,"","setup_converters"],[0,2,1,"","setup_directories"],[0,2,1,"","setup_job_scripts"],[0,2,1,"","setup_listeners"],[0,2,1,"","setup_slurm"],[0,3,1,"","slurm_converters_path"],[0,3,1,"","slurm_data_path"],[0,3,1,"","slurm_images_path"],[0,3,1,"","slurm_model_images"],[0,3,1,"","slurm_model_paths"],[0,3,1,"","slurm_model_repos"],[0,3,1,"","slurm_script_path"],[0,3,1,"","slurm_script_repo"],[0,2,1,"","str_to_class"],[0,2,1,"","transfer_data"],[0,2,1,"","unpack_data"],[0,2,1,"","update_slurm_scripts"],[0,2,1,"","validate"],[0,2,1,"","workflow_params_to_envvars"],[0,2,1,"","workflow_params_to_subs"],[0,2,1,"","zip_data_on_slurm_server"]],"biomero.slurm_client.SlurmJob":[[0,3,1,"","SLURM_POLLING_INTERVAL"],[0,2,1,"","cleanup"],[0,2,1,"","completed"],[0,3,1,"","error_message"],[0,2,1,"","get_error"],[0,3,1,"","job_id"],[0,3,1,"","job_state"],[0,3,1,"","ok"],[0,3,1,"","progress"],[0,3,1,"","slurm_polling_interval"],[0,3,1,"","submit_result"],[0,3,1,"","task_id"],[0,2,1,"","wait_for_completion"],[0,3,1,"","wf_id"]],biomero:[[0,0,0,"-","slurm_client"]]},objnames:{"0":["py","module","Python module"],"1":["py","class","Python class"],"2":["py","method","Python method"],"3":["py","attribute","Python attribute"]},objtypes:{"0":"py:module","1":"py:class","2":"py:method","3":"py:attribute"},terms:{"0":[1,3],"00":[3,4],"001":4,"01":[0,4],"02":4,"03":4,"04":4,"05":3,"06":4,"08":[3,4],"09":3,"1":[0,1,3],"10":[0,3,4],"100":[3,4],"1000":3,"1006116864":4,"1006305280":4,"10802":4,"10gb":[3,4],"10x":3,"117":4,"12":4,"12345":0,"126":4,"12m":4,"13":4,"1336":4,"13t17":4,"15":[3,4],"15gb":[3,4],"16":4,"17":4,"172":4,"18":4,"18gb":4,"1g":[3,4],"2":[0,1,3],"2014":4,"2017":4,"2020":3,"2022":4,"2023":[0,4],"2024":4,"21":[3,4],"22":[3,4],"2215916":4,"2222":4,"224":3,"224x224":3,"2269097984":4,"23":4,"23t08":4,"23t09":4,"24":4,"25":[3,4],"256x256":4,"27":4,"28":4,"2a":4,"2aoamjs0":4,"2b":4,"2c":4,"3":[1,3],"30":[3,4],"300":4,"31":4,"3184":4,"32":[3,4],"33":4,"3358":4,"34":4,"3406":4,"3500":4,"36":4,"37":4,"3a":4,"3b":1,"3c":4,"3m":4,"4":[1,3],"40":4,"4064":4,"4080":4,"4096":4,"41":4,"42":4,"43":4,"44":4,"45":[3,4],"45min":3,"46":4,"4672820":4,"4784967680":4,"48":4,"4j":3,"4x":4,"5":[1,3],"50":3,"5120":4,"52":4,"54":4,"5gb":4,"6":[1,3],"60":3,"600":4,"64":3,"6817":4,"695":4,"7":[3,4],"700":4,"777":4,"7zip":[1,3],"8":[3,4],"9":[3,4],"900":4,"982536":4,"982720":4,"997":3,"case":[3,4],"class":[0,1],"default":[0,3,4],"do":[3,4],"export":3,"final":[0,4],"float":0,"function":[0,3,4],"import":[1,3],"int":0,"long":[3,4],"new":[0,1,4],"null":4,"public":[3,4],"return":[0,3,4],"short":[3,4],"static":4,"true":[0,3,4],"try":[0,1,3],"var":4,"while":[0,3,4],A:[0,3],And:[3,4],As:4,At:[3,4],But:[3,4],By:[3,4],For:[3,4],IS:4,IT:4,If:[0,3,4],In:[3,4],It:[0,3,4],NOT:4,No:4,ONE:3,Of:4,On:4,One:[0,4],Or:[3,4],THAT:4,That:4,The:[0,3,4],Then:[3,4],There:4,These:[0,3,4],To:[3,4],WITH:0,Will:[0,4],With:3,_:3,__:4,_______:4,_______________________________________:4,__init__:3,__main__:[3,4],__name__:[3,4],_aggreg:4,_cellexpans:4,_cp_mask:3,_cpmask:4,_default:0,_imag:4,_job:3,_job_:3,_job_cpu:4,_mask_c1:4,_out_sep:0,_repo:[3,4],abl:4,about:[0,4],abov:[3,4],accept:[0,4],access:[1,3],accomplish:3,accord:[0,3,4],account:[0,1,3],acct:4,action:4,activ:[0,4],actual:[3,4],ad:[0,3,4],adapt:4,add:1,addendum:1,addit:[0,3],addition:3,address:[0,4],adjust:4,admin:3,advanc:4,after:[0,3,4],afterward:[3,4],ag:4,again:[3,4],aggreg:4,algorithm:4,alia:[3,4],aliv:4,all:[0,3,4],allow:[3,4],along:4,alreadi:[0,3,4],also:[0,3,4],altern:0,alwai:[3,4],am:4,amc:4,amount:4,amsterdam:[3,4],an:[0,1,4],analysi:[1,4],analyt:0,analyz:4,ani:[0,3,4],annot:4,anoth:[3,4],anyon:4,anyth:4,anywai:[0,4],anywher:4,apach:4,api:4,app:4,appar:4,append:3,appli:[3,4],applic:4,approach:4,appropri:[0,4],apptain:[1,3],apt:4,ar:[0,3,4],archiv:0,arg:0,argument:[0,4],argv:[3,4],around:4,arrai:0,art:4,asctim:3,ask:[3,4],assign:4,associ:[0,3,4],assum:[0,3,4],astyp:4,attach:[3,4],attack:4,attempt:0,attribut:[0,3],aug:4,authent:[3,4],authorized_kei:4,autom:[3,4],automat:[0,3,4],avail:[0,3,4],azur:1,azureadmin:4,azureus:4,b:3,back:[3,4],base:[0,3,4],base_path:4,bash:4,bashrc:4,basic:3,basicconfig:3,batch:1,becam:4,becaus:[3,4],becom:4,been:[3,4],befor:[0,4],behavior:0,behaviour:4,being:[0,4],below:[0,3,4],benefici:3,best:3,better:[3,4],between:[0,3,4],bfimg:3,bi:1,biaflow:[3,4],biaflowsjob:[3,4],big:4,biggest:4,bimg:3,bin:[3,4],binari:4,bioformats2raw:3,bioimag:[1,4],biomerostorag:4,biomerowork:4,bit:4,bitbucket:3,bj:[3,4],blob:[0,4],blog:4,blosc:3,bonu:4,bool:[0,4],borrow:4,both:[3,4],boutiqu:3,box:4,branch:[0,3,4],brief:3,bring:4,bring_listener_uptod:0,browser:4,bsst265:4,bugfix:4,build:[0,3,4],builddir:4,built:[3,4],bump:4,button:4,c1:4,c2:4,cacert:4,calcul:1,call:[3,4],can:[0,3,4],cancel:0,candl:4,cannot:0,cat:4,caus:4,cc:4,cd:[0,3,4],cell:[0,3,4],cell_diamet:0,cellexpans:1,cellexpansion_job:4,cellexpansion_repo:4,cellnumgranul:4,cellpos:[0,1,3],cellpose_imag:4,cellpose_job:[3,4],cellpose_job_cpu:4,cellpose_job_gr:[3,4],cellpose_job_mem:[3,4],cellpose_job_tim:3,cellpose_mask:4,cellpose_repo:[3,4],cellpose_v1:4,cellposemask:4,cellprob_threshold:[3,4],cellprofil:[1,3],cellprofiler_job:4,cellprofiler_repo:4,cellprofiler_result:4,cellprofiler_spot:4,cellprofiler_spot_job:4,cellprofiler_spot_repo:4,cellprofiler_v1:4,cells_aggreg:4,cells_cellexpans:4,cellsgranuleslabel:4,cellsnucleilabel:4,cellular:[3,4],cellularimagingcf:3,centroid:4,certif:4,cetera:3,cf:4,challeng:4,chan:[3,4],chang:[3,4],channel:[0,3,4],chapter:[3,4],cheap:4,cheaper:4,check:[0,3,4],check_job_statu:0,checkout:4,chmod:4,choos:4,chosen:[3,4],chown:4,chunk:3,ci:4,class_nam:0,class_objseg:4,classmethod:0,clean:4,cleanup:0,cleanup_tmp_fil:0,cli:3,click:4,client:[0,1,3],clone:[0,3,4],close:4,closesess:4,cloud:[1,3],cluster:[0,3],cluster_kei:4,cmd:[3,4],cmdlist:0,code:[1,4],coffe:[3,4],color:4,column:[0,4],com:[0,3,4],combin:4,come:[3,4],comma:0,command:[0,3],commandlin:[3,4],comment:[3,4],commerci:4,commit:4,commmand:4,common:4,commonwl:3,commun:4,compat:3,complet:[0,4],compon:4,compos:4,comput:[3,4],concaten:0,concept:0,conf:4,config:[0,1,4],config_fil:0,config_omero_:3,config_omero_logging_level:3,config_omero_master_host:3,config_onli:0,configfil:[0,3,4],configur:[0,3,4],congratul:[3,4],conn:0,connect:[0,3,4],connect_kwarg:0,connect_timeout:0,connectionlostexcept:4,consecut:0,consist:3,consol:[3,4],constant:4,constructor:0,contain:[0,1],container:3,container_nam:[3,4],content:[3,4],context:4,contextmanag:0,continu:4,contributor:4,control:4,conveni:3,convers:0,convert:[0,3,4],convert_cytype_to_omtyp:0,convert_job_arrai:4,convert_url:0,converter_imag:0,copi:[0,3,4],copy_zip_loc:[0,3],copyleft:4,copyright:4,core:[3,4],correct:4,correctli:[3,4],correspond:[0,3],cost:[3,4],could:[0,3,4],count:4,count_nonzero:4,cours:[3,4],cover:4,cow:4,cp:[3,4],cp_model:[0,3],cppipe:4,cpproj:4,cpu:[3,4],creat:[0,3],creating_bia_workflow_and_adding_to_biaflows_inst:4,creation:0,credenti:4,credit:4,creditcard:4,crop:3,crt:4,csv:4,ctld:4,ctrl:4,current:[0,3,4],custom:1,cv2:4,cwd:3,cyclecloud:4,cython:4,cytomin:[0,3,4],cytomine_:3,cytomine_host:4,cytomine_id_project:4,cytomine_id_softwar:4,cytomine_job:0,cytomine_private_kei:4,cytomine_public_kei:4,cytoplasm:4,cytyp:0,d:[0,3],da:4,daemon:4,danger:4,data:[0,1],data_loc:0,data_path:[0,3],databas:0,datadisk:3,datafil:4,datafram:4,dataset:[3,4],date:[3,4],db:1,dbd:4,dbformysql:4,dd:0,de:4,debug:[3,4],deepcel:[3,4],deepcell_job:4,deepcell_repo:4,def:4,defin:[3,4],definit:[0,4],deleg:4,delet:[3,4],demand:4,deni:4,depend:[0,3],depends_on:4,deploi:[3,4],deploy:4,depth:3,deriv:4,descend:0,describ:[3,4],descript:[3,4],descriptor:[0,1],desir:3,desktop:4,destin:4,destroi:4,detail:[3,4],detect:0,dev:[3,4],devel:3,develop:4,diamet:[0,3,4],dict:0,dictionari:0,did:4,didn:4,differ:[3,4],digicert:4,digicertglobalrootca:4,dimens:3,dir:[3,4],directli:[3,4],directori:[0,3,4],dirti:4,discuss:3,distinguish:0,distribut:4,dl:[0,4],dn:4,doc:4,docker:[0,1],dockerfil:3,dockerfile_slurmctld:4,dockerhub:[0,3],dockerhub_token:4,dockerhub_usernam:4,docstr:3,document:[0,4],doe:[0,4],doesn:[0,3,4],don:[3,4],done:[3,4],dot:4,down:[3,4],download:[0,3,4],drastic:4,drive:[3,4],drop:0,drwxr:4,drwxrwxr:4,ds:4,dtype:4,dunde:4,dure:0,dyn:4,dynam:4,e:[0,3],each:[0,3,4],earlier:3,easi:[3,4],easier:[3,4],easiest:[0,3,4],easili:4,eavesdrop:4,echo:[3,4],edit:4,editor:4,effect:4,effici:3,either:[0,3,4],elaps:4,els:[0,3],email:[0,3,4],embarrassingli:3,empti:[0,4],en:4,enabl:[0,3],enable_job_account:0,enable_job_progress:0,enable_workflow_analyt:0,encapsul:0,encount:0,encourag:[3,4],end:[0,3,4],end_tim:0,endtim:4,enforc:3,enhanc:4,enjoi:4,enough:[3,4],ensur:[0,3,4],enter:4,entri:[0,4],entrypoint:[3,4],env:[0,4],environ:[0,3,4],equal:3,equip:3,err_desc:3,error:[0,3,4],error_messag:0,escap:4,especi:[3,4],essenti:4,estim:4,et:3,etc:[0,3,4],etc_mung:4,etc_slurm:4,etric:4,euro:4,europ:4,even:[3,4],everi:[3,4],everybodi:4,ex:4,exampl:[0,3,4],excel:4,except:[0,4],exec:4,execut:[0,3,4],exercis:4,exist:[0,1,4],exit:[3,4],expect:[0,3,4],expens:[3,4],expire_tim:4,explain:4,explan:3,explicitli:3,explor:[3,4],expos:4,ext:4,extend:[0,3],extens:[0,4],extern:[3,4],extra:[1,3],extract:[0,1],extract_data_location_from_log:0,extract_job_id:0,extract_parts_from_url:0,ezomero:3,f:[0,3,4],fabric:[0,3,4],facil:3,fact:3,fail:[0,3,4],failur:0,fair:[1,3],fals:[0,4],faster:[3,4],favorit:4,featur:3,few:4,field:3,figur:3,fiji:3,file:[0,3],filenam:[0,3],filename_no_extens:3,filepath:4,fileserv:4,filetyp:0,fill:[0,4],filler:4,filter:[0,4],filter_filetyp:0,find:[0,3,4],fine:4,finish:3,fire:4,firewal:4,first:[0,3,4],fit:4,fix:[0,4],flag:[0,3,4],flexibl:[3,4],flexibleserv:4,fluorescens:4,folder:[0,3,4],folder_nam:0,folk:4,follow:[0,3,4],forc:0,force_upd:0,forget:4,form:[3,4],format:[0,3,4],forward:[3,4],forward_ag:0,found:[0,3,4],framework:3,free:[3,4],friendli:3,from:[0,1,3],from_cli:[3,4],from_config:[0,3,4],full:[0,4],fulli:4,fun:[3,4],funni:4,futur:[0,3,4],fw:4,g:[0,3,4],gain:4,gatewai:[0,4],gb:[3,4],gcloud:4,gcslurm:4,gener:[0,1,4],generate_job:[0,3],generate_slurm_job_for_workflow:0,get:[0,4],get_active_job_progress:0,get_all_image_versions_and_data_fil:[0,4],get_cellpose_command:0,get_conversion_command:0,get_error:0,get_image_versions_and_data_fil:0,get_job_status_command:0,get_jobs_info_command:0,get_listen:0,get_logfile_from_slurm:[0,3],get_or_create_github_sess:0,get_recent_log_command:0,get_unzip_command:0,get_update_slurm_scripts_command:0,get_workflow_command:0,get_workflow_paramet:0,get_zip_command:0,getenv:4,getinput:4,getlogg:4,ghpc:4,giant:4,gid:3,giovtorr:4,git:[0,3,4],github:[0,3],give:[0,3,4],given:[0,3,4],global:3,gnu:4,go:4,godlovedc:4,good:4,googl:1,gosu:4,got:4,gpu:[0,1,4],grab:[1,3],granuleslabel:4,granulesstat:4,granulesstatsincelllabel:4,granulesstatsnp:4,grayscal:3,gre:4,great:4,grei:3,grid:4,ground:3,group:4,groupadd:4,gt:4,gt_img:[3,4],gt_path:[3,4],gtfolder:[3,4],guid:[3,4],gz:4,ha:[0,3,4],had:4,half:4,hand:4,handl:[3,4],handout:4,hardcod:[3,4],hardwar:3,have:[0,3,4],headbash:4,header:0,headless:3,heard:4,hello:3,help:3,helper:4,here:[3,4],hh:[0,3],hidden:4,high:3,higher:3,highli:4,hoc:4,hold:4,home:[3,4],hope:4,hopefulli:[3,4],host:[0,3,4],hostnam:[3,4],hour:3,how:1,howev:[0,3,4],hpc:[3,4],hpcsmall:4,htc:4,html:[3,4],htop:4,http:[0,3,4],hub:4,human:4,i:[1,4],iap:4,ic:4,id:[0,3,4],id_rsa:[3,4],idea:4,ideal:4,identif:4,identityfil:4,idkei:4,idl:4,ignor:[3,4],ij:3,ij_min_threshold:3,ij_radiu:3,ijm:3,imag:[0,3],image_nam:0,image_path:3,image_tag:4,image_vers:[0,3],imageio:3,imagej:[3,4],imagej_job:4,imagej_repo:4,imcellscelllabel:4,imcellsgranuleslabel:4,img:3,implement:[0,3,4],improv:[3,4],imread:[3,4],imread_anydepth:4,imwrit:3,in_img:[3,4],in_path:[3,4],inbound:4,incl:3,includ:[0,3,4],incur:3,indefinit:3,index:[0,1],indic:0,individu:0,infinit:4,info:[0,3,4],infold:[3,4],inform:[0,3,4],ingredi:4,ingress:4,ini:[0,1,4],init:[3,4],init_environ:4,init_slurm:[0,3,4],init_workflow:0,initi:[0,4],initialis:4,initialize_analytics_system:0,initscript:4,inject:3,inline_ssh_env:0,innodb_lock_wait_timeout:4,input:[0,3,4],input_data:0,input_fold:3,input_url:0,insert:4,insid:4,insight:[3,4],instal:[1,3],instanc:[0,3,4],instanti:[0,4],instead:[0,3,4],insuffici:4,int16:4,integr:[3,4],interact:[0,3,4],interfac:3,intern:4,internet:4,interoper:4,interv:0,introduct:1,invest:4,invok:0,involv:0,io:[3,4],ip:4,is_2d:[3,4],iso:0,isol:3,issu:[0,3,4],its:[0,3,4],jar:3,java:3,job:[0,1,4],job_id:0,job_stat:0,job_templ:[0,3,4],jobid:[0,4],jobnam:4,jobscript:[3,4],join:[3,4],json:[0,1],jump:4,just:[3,4],keep:[3,4],kei:[0,3,4],keygen:4,keyword:0,kickstart:4,kind:4,know:4,knowledg:4,known:[0,4],known_host:3,kwarg:0,la:4,last:[0,4],later:[0,4],latest:[0,3,4],launch:[3,4],law:4,lead:4,learn:4,least:3,leav:4,left:[3,4],less:[3,4],let:4,lethal:3,level:3,levelnam:3,lib:3,libgeo:4,librari:[0,3,4],licens:[1,3],lightweight:4,like:[0,3,4],limit:[0,1,4],line:[0,3,4],linear:4,link:[0,4],linux:4,lisbon:4,list:[0,4],list_active_job:0,list_all_job:0,list_available_converter_vers:0,list_completed_job:0,listen:0,liter:[3,4],ll:4,load:[0,4],local:[0,1,3],local_path:0,local_tmp_storag:0,localhost:[3,4],localslurm:4,locat:[0,3,4],log:[0,1,4],log_fil:0,logfil:[0,3,4],logger:[0,4],logic:4,login:[3,4],logout:4,lolcow:4,longer:[3,4],look:[0,3,4],lose:3,lot:[3,4],lower:4,ls:4,lt:4,luckili:4,luik:4,m:[3,4],mac:4,machin:[0,3,4],macro:3,made:[3,4],mage:3,magic:4,mai:4,mail:[3,4],main:[3,4],mainli:[3,4],major:4,make:[3,4],man:4,manag:[0,1,3],mandatori:[3,4],manipul:4,manual:3,map:[0,4],mar:4,march:4,mask:[1,3],master:[0,3,4],match:[0,3,4],matter:4,max:[3,4],maximum:[0,3],maxshap:3,maxvm:4,mayb:[3,4],mconfig:4,md:4,me:4,mean:4,meant:4,measur:4,mechan:0,medium:3,mem:4,memori:3,mention:0,merchant:4,messag:[0,3,4],metadata:1,method:[0,3,4],metric:[3,4],microscopi:4,microsoft:1,middl:4,might:[0,3,4],min:[3,4],min_threshold:3,mine:4,minim:[3,4],minshap:3,minut:[3,4],miss:[3,4],mkdir:4,mlflow:3,mm:[0,3],mnt:3,mod_pipelin:4,mode:4,model:[0,3,4],model_path:3,modern:4,modifi:4,modul:[1,2,3,4],module_nam:0,moment:4,monei:4,monitor:[0,3],month:4,more:[0,3,4],most:[0,4],mount:[3,4],move:3,movi:4,ms:4,much:4,multipl:[0,1,4],mung:4,must:[0,4],my:[0,3,4],myjob:0,mysql:4,n:[0,4],name:[0,3,4],namespac:4,nasti:4,ndarrai:4,ndata:4,necessari:[0,3],need:[0,3,4],net:4,network:3,neubia:[3,4],newest:4,newli:4,next:[0,3,4],nextflow:4,nf:0,ngc:4,nice:[3,4],nicer:3,nj:3,nl:[3,4],nmc:4,no_npi:[3,4],node:[3,4],nodelist:4,nodenam:4,nologin:4,non:[3,4],none:[0,3],normal:4,note2:3,note:[0,3,4],noth:0,notif:0,now:[0,3,4],np:4,nsdynam:4,nuc:[3,4],nuc_channel:[0,3,4],nuclear:0,nuclei:[0,4],nucleilabel:4,nucleu:4,num:4,number:[0,4],numcel:4,o:[0,1,4],object:[0,3],oblig:4,occur:0,off:4,offer:3,offload:4,ok:[0,4],old:[0,4],older:4,om:3,omero:[0,1],omero_worker_nam:3,omeroconn:0,omeroinsight:4,omeroserv:3,omeroweb:4,omerowork:4,omit:[0,3],omput:4,onc:[3,4],one:[0,3,4],ones:[0,4],onli:[0,3],onlin:4,onto:4,oo:4,op:4,open:4,openssh:4,oper:[0,3,4],opt:[3,4],option:[0,1,3],orchestr:4,order:0,origin:[0,3,4],original_fil:4,os:[3,4],osc:3,oserror:0,other:[0,3,4],otherwis:[0,3,4],our:[3,4],out:[0,3],out_path:[3,4],outfold:[3,4],output:[0,3,4],outsid:4,over:[0,3,4],overal:3,overhead:[3,4],overlap:1,overrid:[3,4],overview:1,overwrit:[0,4],own:[1,4],ownership:4,p7zip:4,p:4,packag:[2,3],package_upgrad:4,page:4,paid:4,pair:[0,4],parallel:[3,4],param:[0,3],param_nam:4,paramet:[0,1],paramiko:0,pars:[0,4],parse_cellprofiler_paramet:4,parse_docker_image_vers:0,parsecpparam:4,part:[0,4],particularli:[0,4],partit:4,pass:0,password:4,passwordless:3,past:4,path:[0,3,4],pattern:0,pd:4,peer:4,pem:4,pend:0,peopl:4,per:[0,3,4],perform:[0,3,4],perhap:[0,3,4],permiss:4,pick:4,pickup:4,pin:3,pip:[3,4],pipelin:[1,3],pitfal:3,pixel:0,pla:4,pla_data:4,place:3,placehold:[0,4],plai:4,plate:4,platform:3,pleas:[3,4],plugin:[3,4],png:4,podman:[3,4],point:[3,4],poll:[0,3],port:[0,3,4],portal:4,posit:0,possibl:[3,4],potenti:3,power:4,ppa:4,practic:[3,4],predict:3,prefix:4,prepar:[3,4],prepare_data:[3,4],preprocess:3,prerequisit:1,present:0,press:4,pretrained_model:[3,4],pretti:4,previou:3,price:4,primit:3,print:[0,3,4],prioriti:4,privat:[3,4],prob:3,prob_thresh:3,prob_threshold:[0,3,4],probabl:[0,4],problem:3,problem_cl:[3,4],proceed:0,process:[0,3,4],processor:[3,4],profil:4,program:[3,4],programmat:3,progress:[0,3,4],project:4,promot:4,promptless:4,proper:4,properli:[0,4],properti:4,protein:4,protocol:4,provid:[0,3,4],pub:[3,4],pubkei:3,publish:3,pull:[0,3,4],pull_descriptor_from_github:0,pull_imag:4,purpos:[0,3,4],push:4,put:[3,4],pw:4,py:[0,1],pypi:3,pytest:3,python3:[3,4],python:[0,1,4],quantifi:4,queri:0,queue:4,quick:[3,4],quicker:4,quickstart:1,quit:4,r:[0,4],radiu:3,rais:[0,3],ran:4,rang:4,raw:[0,4],re:4,reach:[0,4],read:[0,3],readabl:4,reader:4,readi:4,readm:4,realli:4,realmemori:4,reason:4,rebuild:4,receiv:0,recent:[0,4],recogn:4,recommend:3,recreat:[0,4],reduc:4,refer:[0,3,4],referenc:3,refresh:[3,4],region:4,regionprops_t:4,registr:4,rel:4,relat:[0,3,4],releas:[3,4],remain:[0,4],remot:[0,3,4],remov:[0,4],renam:4,replac:[3,4],repo:[0,3,4],repositori:[0,3],repres:0,reproduc:[3,4],request:[3,4],requir:[0,1],reserv:4,reset_t:0,resiz:3,resourc:[3,4],respons:0,rest:4,restart:4,restrict:4,result:[0,3,4],retain:[0,4],retri:0,retriev:[0,3,4],return_cod:3,returncod:3,reus:4,review:3,rewrit:3,rewrot:4,rgb:3,rich:4,right:4,rm:[3,4],rocki:4,rockylinux:4,role:4,root:4,rootless:4,round:4,row:4,rs:0,rstring:4,rtype:4,rule:4,run:[0,1,3],run_command:0,run_commands_split_out:0,run_conversion_workflow_job:0,run_workflow:[0,4],run_workflow_job:0,runcmd:4,runner:[0,4],runscript:[3,4],runtim:3,rw:4,rwxr:4,s:[0,3,4],sacct:[0,4],sadli:4,safe:4,sai:[3,4],same:[0,3,4],satisfi:4,save:4,save_tif:[3,4],sbatch:[0,3,4],sbin:4,sc:3,scale:4,scenario:3,schedmd:3,schedul:[3,4],schema:[1,4],scheme:3,scp:[0,3,4],scratch:[0,4],screen:[3,4],script:[0,1],scroll:4,second:[0,4],secret:[3,4],section:[3,4],secur:4,see:[0,1,4],seem:4,segment:[3,4],select:[3,4],send:[0,3],sep:0,separ:[0,4],seriou:4,server:[0,3,4],servic:4,session:0,set:[0,1,3],setoutput:4,setup:[0,1,3],setup_container_imag:0,setup_convert:0,setup_directori:0,setup_job_script:0,setup_listen:0,setup_slurm:0,sever:[3,4],sftp:3,sh:[0,3,4],shakespear:4,shame:4,shape:3,share:[0,3,4],sharg:4,shell:[0,3,4],shenanigan:4,shorter:3,should:[1,3],shoulder:4,show:[3,4],shown:4,showtim:1,shutil:3,side:4,sif:[0,3,4],sign:4,similar:[0,4],simpl:[0,3,4],simpli:3,simplifi:[3,4],sinc:4,sing:4,singl:0,singular:[0,1,3],singularity_imag:[0,3,4],singularity_vers:4,size:4,sleep:4,slow:3,slurm:[0,1],slurm_cellpose_segment:3,slurm_client:[1,2],slurm_config:4,slurm_converters_path:0,slurm_data_path:[0,3,4],slurm_images_path:[0,3,4],slurm_job_id:0,slurm_jobdir:4,slurm_model_imag:0,slurm_model_job:0,slurm_model_jobs_param:0,slurm_model_path:0,slurm_model_repo:0,slurm_polling_interv:0,slurm_run_workflow_batch:4,slurm_script_path:[0,3,4],slurm_script_repo:[0,3,4],slurmclient:[0,1,4],slurmctld:4,slurmdbd:4,slurmjob:0,small:4,smaller:[3,4],smart:[3,4],snakemak:4,so:[3,4],softwar:[3,4],solut:4,some:[0,3,4],someon:4,someth:[3,4],sort:0,sound:4,sourc:[0,3,4],source_format:0,south:4,space:[0,4],specif:[0,3,4],specifi:[0,3],speckl:4,speed:[3,4],speedup:4,spent:4,spin:[3,4],split:[0,4],spot:4,spotcount:4,spun:4,sqlalchemy_url:0,squeue:4,ss:[0,3],ssh:[0,1],sshd:4,sshdocker:4,sshexcept:0,sshgroup:4,sshuser:4,ssl:4,st:4,stai:[3,4],stain:4,stand:4,standard:3,standard_dc2s_v3:4,standard_dc4s_v3:4,standard_nd96amsr_a100_v4:4,stardist:[3,4],stardist_job:4,stardist_repo:4,start:[0,4],start_tim:0,starttim:4,state:[0,4],statu:[0,3,4],statuscom:[3,4],stdout:[0,3,4],step:[3,4],stick:4,still:[0,4],storag:[0,4],storageaccount:4,store:[0,3,4],str:[0,4],str_to_class:0,stream:3,stricthostkeycheck:4,strictli:3,string:[0,3,4],strong:3,strongli:4,stuff:4,style:4,sub:0,subdirectori:4,subfold:[0,4],subject:4,submiss:[0,3,4],submit:[0,3,4],submit_result:0,submitit:3,subprocess:[3,4],subscript:4,substitut:0,succeed:0,success:[0,4],successfulli:0,sudo:4,suffix:4,suit:4,superus:4,suppli:4,support:[0,3,4],sure:[3,4],sweet:4,sy:3,system:[0,4],systemctld:4,t:[0,3,4],t_nucleisegment:4,t_t_luik:4,t_t_luik_amsterdamumc_nl:4,tab:[3,4],tabl:4,tag:[0,3,4],tail:[3,4],take:[0,3,4],tar:4,target:[0,3],target_format:0,task:[0,3,4],task_id:0,tbc:3,tcp:4,tell:4,templat:[0,3,4],temporari:[0,4],term:4,termin:[3,4],test:1,testproject:4,text:[3,4],than:[3,4],thei:[3,4],them:[0,3,4],themselv:[0,4],theoret:3,theori:[3,4],thi:[0,1,3],thing:4,think:[3,4],third:4,those:[0,3,4],though:4,thought:1,threshold:[0,3,4],through:[3,4],thrown:4,tick:4,tif:[0,3,4],tiff:[0,3,4],tifffil:3,time:[0,1,4],timelimit:4,timeout:[0,3],tischi:4,tmp:[0,3],tmp_path:[3,4],to_numpi:4,togeth:[3,4],token:4,too:1,took:4,tool:0,top:4,torec:4,torecluik:[3,4],total:4,touch:4,toward:3,track:[0,4],track_workflow:0,trailer:0,transfer:[0,1],transfer_data:[0,3],transferresult:0,tree:[3,4],trick:4,troubl:4,trust:[3,4],truth:3,truthi:0,tue:4,tune:4,tupl:0,turn:[3,4],twice:4,two:0,txt:[3,4],type:[0,4],u:4,ubuntu:4,ui:[1,3],uid:3,uint16:4,uk:4,ulieg:[0,4],umc:[3,4],uncheck:[3,4],under:[3,4],understand:4,uniform:3,uniqu:[0,3,4],univers:4,unknown:4,unless:[3,4],unlik:0,unpack:[0,3],unpack_data:[0,3],until:[0,3],unvers:0,unwrap:4,unzip:[0,3],up:[0,1,3],updat:[0,3],update_slurm_script:[0,3],upgrad:4,upload:[1,3],url:[0,4],us:[0,1],use_gpu:[0,3,4],user:[0,3,4],useradd:4,userknownhostsfil:4,usern:3,usernam:[3,4],usr:[3,4],utf:4,util:[3,4],util_script:4,uuid:0,v0:4,v1:[3,4],v2:4,v3:4,v:4,valid:[0,3,4],validate_slurm_setup:[0,3,4],valu:[0,3,4],valueerror:[0,3],var_log_slurm:4,variabl:[0,3,4],variou:3,ve:4,venic:4,venv:[3,4],venvtest:3,veri:[3,4],verifi:4,version:[0,1,4],vi:4,via:[0,1,4],video:4,view:[0,4],vm:4,vnet:4,volum:[3,4],vs:4,w:[3,4],w_cellexpans:4,w_cellexpansion_v2:4,w_countmaskoverlap:4,w_countmaskoverlap_v1:4,w_nucleisegment:[3,4],w_spotcount:4,wa:[0,4],wai:[0,3,4],wait:[0,3,4],wait_for_complet:0,walk:4,want:[3,4],warn:[0,3,4],watch:3,we:[0,1,3],web:[1,3],websit:[3,4],wed:4,well:[3,4],were:4,western:4,wf:4,wf_id:0,wg5:4,wget:4,what:[0,3,4],whatev:4,when:[0,3,4],whenev:4,where:[0,3,4],whether:0,which:[0,3,4],whole:4,william:4,window:[3,4],within:[0,3,4],without:[0,4],won:4,work:[0,3,4],worker:4,workflow:[0,1],workflow_nam:0,workflow_params_to_envvar:0,workflow_params_to_sub:0,workflow_vers:0,workload:[0,4],world:3,worth:0,would:[3,4],wq:4,wrap:[3,4],wrapper:1,write:[3,4],wrong:4,wrote:4,x:[0,4],xmx6000m:3,xr:4,xvfb:3,xzf:4,y:[3,4],ye:4,yet:[0,3,4],yml:[0,3,4],you:[0,3,4],your:[0,1],yourself:3,yum:[3,4],yyyi:0,zarr:[0,3],zero:4,zip:[0,3,4],zip_data_on_slurm_serv:[0,3],zipfil:[0,4]},titles:["biomero package","Welcome to BIOMERO\u2019s documentation!","biomero","BIOMERO - BioImage analysis in OMERO","Cellprofiler tutorial"],titleterms:{"0":4,"1":4,"2":4,"3":4,"3b":4,"4":4,"5":4,"6":4,"7zip":4,"class":3,"export":4,"import":4,"new":3,"try":4,A:4,access:4,account:4,add:[3,4],addendum:4,altern:4,an:3,analysi:3,apptain:4,azur:4,b:4,basic:4,batch:[3,4],bi:4,bioimag:3,biomero:[0,1,2,3,4],c:4,calcul:4,cellexpans:4,cellpos:4,cellprofil:4,client:4,cloud:4,cluster:4,code:3,command:4,config:3,contain:[3,4],creat:4,custom:3,d:4,data:[3,4],databas:4,db:4,descriptor:[3,4],docker:[3,4],dockerfil:4,dockerhub:4,document:1,dr:4,e:4,exist:3,extra:4,extract:4,fair:4,file:4,from:4,gener:3,get:[1,3],github:4,googl:4,gpu:3,grab:4,headless:4,how:[3,4],i:3,imag:4,indic:1,ini:3,instal:4,introduct:4,job:3,json:[3,4],licens:4,limit:3,local:4,log:3,manag:4,manual:4,mask:4,memori:4,metadata:[3,4],microsoft:4,modul:0,multipl:3,network:4,o:3,omero:[3,4],onli:4,option:4,out:4,overlap:4,overview:3,own:3,packag:[0,1,4],paramet:[3,4],pipelin:4,prerequisit:[3,4],publish:4,py:[3,4],python:3,quickstart:3,repositori:4,requir:[3,4],run:4,s:1,schema:3,script:[3,4],see:3,set:4,setup:4,should:4,showtim:4,singular:4,slurm:[3,4],slurm_client:0,slurmclient:3,ssh:[3,4],start:[1,3],subnet:4,suggest:4,tabl:1,test:[3,4],thi:4,thought:4,time:3,tl:4,too:4,transfer:3,tutori:[1,3,4],ui:4,up:4,updat:4,upload:4,us:[3,4],version:3,via:3,virtual:4,we:4,web:4,welcom:1,workflow:[3,4],wrapper:[3,4],your:[3,4]}})
\ No newline at end of file