diff --git a/_sources/source/guides/installation_guide.rst b/_sources/source/guides/installation_guide.rst index 54c93af8..61f03677 100644 --- a/_sources/source/guides/installation_guide.rst +++ b/_sources/source/guides/installation_guide.rst @@ -110,3 +110,54 @@ OR to install from source: .. code-block:: pip install -e . + +Optional requirements +--------------------- + +Additional functionalities +~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +Several additional functionalities are available optionally. To install them, use the following commands: + +- CRF post-processing: + +.. code-block:: + + pip install pydensecrf@git+https://github.com/lucasb-eyer/pydensecrf.git#egg=master + +- Weights & Biases integration: + +.. code-block:: + + pip install napari-cellseg3D[wandb] + + +- ONNX model support (EXPERIMENTAL): + Depending on your hardware, you can install the CPU or GPU version of ONNX. + +.. code-block:: + + pip install napari-cellseg3D[onnx-cpu] + pip install napari-cellseg3D[onnx-gpu] + +Development requirements +~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +- Building the documentation: + +.. code-block:: + + pip install napari-cellseg3D[docs] + +- Running tests locally: + +.. code-block:: + + pip install pydensecrf@git+https://github.com/lucasb-eyer/pydensecrf.git#egg=master + pip install napari-cellseg3D[test] + +- Dev utilities: + +.. code-block:: + + pip install napari-cellseg3D[dev] diff --git a/objects.inv b/objects.inv index 0d094715..ccfdd547 100644 Binary files a/objects.inv and b/objects.inv differ diff --git a/searchindex.js b/searchindex.js index 044b7f2d..40cd61dc 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({docnames:["TODO","source/code/_autosummary/napari_cellseg3d.code_models","source/code/_autosummary/napari_cellseg3d.code_models.crf","source/code/_autosummary/napari_cellseg3d.code_models.instance_segmentation","source/code/_autosummary/napari_cellseg3d.code_models.model_framework","source/code/_autosummary/napari_cellseg3d.code_models.models","source/code/_autosummary/napari_cellseg3d.code_models.models.TEMPLATE_model","source/code/_autosummary/napari_cellseg3d.code_models.models.model_SegResNet","source/code/_autosummary/napari_cellseg3d.code_models.models.model_SwinUNetR","source/code/_autosummary/napari_cellseg3d.code_models.models.model_TRAILMAP","source/code/_autosummary/napari_cellseg3d.code_models.models.model_TRAILMAP_MS","source/code/_autosummary/napari_cellseg3d.code_models.models.model_VNet","source/code/_autosummary/napari_cellseg3d.code_models.models.model_WNet","source/code/_autosummary/napari_cellseg3d.code_models.models.model_test","source/code/_autosummary/napari_cellseg3d.code_models.models.pretrained","source/code/_autosummary/napari_cellseg3d.code_models.models.unet","source/code/_autosummary/napari_cellseg3d.code_models.models.unet.buildingblocks","source/code/_autosummary/napari_cellseg3d.code_models.models.unet.model","source/code/_autosummary/napari_cellseg3d.code_models.models.wnet","source/code/_autosummary/napari_cellseg3d.code_models.models.wnet.model","source/code/_autosummary/napari_cellseg3d.code_models.models.wnet.soft_Ncuts","source/code/_autosummary/napari_cellseg3d.code_models.worker_inference","source/code/_autosummary/napari_cellseg3d.code_models.worker_training","source/code/_autosummary/napari_cellseg3d.code_models.workers_utils","source/code/_autosummary/napari_cellseg3d.code_plugins","source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_base","source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_convert","source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_crf","source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_crop","source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_helper","source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_metrics","source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_model_inference","source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_model_training","source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_review","source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_review_dock","source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_utilities","source/code/_autosummary/napari_cellseg3d.interface","source/code/_autosummary/napari_cellseg3d.utils","source/code/api","source/guides/cropping_module_guide","source/guides/custom_model_template","source/guides/detailed_walkthrough","source/guides/inference_module_guide","source/guides/installation_guide","source/guides/metrics_module_guide","source/guides/review_module_guide","source/guides/training_module_guide","source/guides/training_wnet","source/guides/utils_module_guide","welcome"],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,"sphinxcontrib.bibtex":9,sphinx:56},filenames:["TODO.md","source/code/_autosummary/napari_cellseg3d.code_models.rst","source/code/_autosummary/napari_cellseg3d.code_models.crf.rst","source/code/_autosummary/napari_cellseg3d.code_models.instance_segmentation.rst","source/code/_autosummary/napari_cellseg3d.code_models.model_framework.rst","source/code/_autosummary/napari_cellseg3d.code_models.models.rst","source/code/_autosummary/napari_cellseg3d.code_models.models.TEMPLATE_model.rst","source/code/_autosummary/napari_cellseg3d.code_models.models.model_SegResNet.rst","source/code/_autosummary/napari_cellseg3d.code_models.models.model_SwinUNetR.rst","source/code/_autosummary/napari_cellseg3d.code_models.models.model_TRAILMAP.rst","source/code/_autosummary/napari_cellseg3d.code_models.models.model_TRAILMAP_MS.rst","source/code/_autosummary/napari_cellseg3d.code_models.models.model_VNet.rst","source/code/_autosummary/napari_cellseg3d.code_models.models.model_WNet.rst","source/code/_autosummary/napari_cellseg3d.code_models.models.model_test.rst","source/code/_autosummary/napari_cellseg3d.code_models.models.pretrained.rst","source/code/_autosummary/napari_cellseg3d.code_models.models.unet.rst","source/code/_autosummary/napari_cellseg3d.code_models.models.unet.buildingblocks.rst","source/code/_autosummary/napari_cellseg3d.code_models.models.unet.model.rst","source/code/_autosummary/napari_cellseg3d.code_models.models.wnet.rst","source/code/_autosummary/napari_cellseg3d.code_models.models.wnet.model.rst","source/code/_autosummary/napari_cellseg3d.code_models.models.wnet.soft_Ncuts.rst","source/code/_autosummary/napari_cellseg3d.code_models.worker_inference.rst","source/code/_autosummary/napari_cellseg3d.code_models.worker_training.rst","source/code/_autosummary/napari_cellseg3d.code_models.workers_utils.rst","source/code/_autosummary/napari_cellseg3d.code_plugins.rst","source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_base.rst","source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_convert.rst","source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_crf.rst","source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_crop.rst","source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_helper.rst","source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_metrics.rst","source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_model_inference.rst","source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_model_training.rst","source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_review.rst","source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_review_dock.rst","source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_utilities.rst","source/code/_autosummary/napari_cellseg3d.interface.rst","source/code/_autosummary/napari_cellseg3d.utils.rst","source/code/api.rst","source/guides/cropping_module_guide.rst","source/guides/custom_model_template.rst","source/guides/detailed_walkthrough.rst","source/guides/inference_module_guide.rst","source/guides/installation_guide.rst","source/guides/metrics_module_guide.rst","source/guides/review_module_guide.rst","source/guides/training_module_guide.rst","source/guides/training_wnet.rst","source/guides/utils_module_guide.rst","welcome.rst"],objects:{"napari_cellseg3d.code_models":[[2,0,0,"-","crf"],[3,0,0,"-","instance_segmentation"],[4,0,0,"-","model_framework"],[5,0,0,"-","models"],[21,0,0,"-","worker_inference"],[22,0,0,"-","worker_training"],[23,0,0,"-","workers_utils"]],"napari_cellseg3d.code_models.models":[[6,0,0,"-","TEMPLATE_model"],[7,0,0,"-","model_SegResNet"],[8,0,0,"-","model_SwinUNetR"],[9,0,0,"-","model_TRAILMAP"],[10,0,0,"-","model_TRAILMAP_MS"],[11,0,0,"-","model_VNet"],[12,0,0,"-","model_WNet"],[13,0,0,"-","model_test"],[14,0,0,"-","pretrained"],[15,0,0,"-","unet"],[18,0,0,"-","wnet"]],"napari_cellseg3d.code_models.models.unet":[[16,0,0,"-","buildingblocks"],[17,0,0,"-","model"]],"napari_cellseg3d.code_models.models.wnet":[[19,0,0,"-","model"],[20,0,0,"-","soft_Ncuts"]],"napari_cellseg3d.code_plugins":[[25,0,0,"-","plugin_base"],[26,0,0,"-","plugin_convert"],[27,0,0,"-","plugin_crf"],[28,0,0,"-","plugin_crop"],[29,0,0,"-","plugin_helper"],[30,0,0,"-","plugin_metrics"],[31,0,0,"-","plugin_model_inference"],[32,0,0,"-","plugin_model_training"],[33,0,0,"-","plugin_review"],[34,0,0,"-","plugin_review_dock"],[35,0,0,"-","plugin_utilities"]],napari_cellseg3d:[[1,0,0,"-","code_models"],[24,0,0,"-","code_plugins"],[36,0,0,"-","interface"],[37,0,0,"-","utils"]]},objnames:{"0":["py","module","Python module"]},objtypes:{"0":"py:module"},terms:{"0":[41,42,44,47,48,49],"00915":2,"019":49,"0554":49,"08506":[2,19,20,49],"1":[39,40,41,42,44,47,49],"10":49,"100":[46,47],"1038":49,"120":41,"128":[41,46],"1606":2,"1711":[2,19,20,49],"1e":[41,47],"2":[39,41,42,43,44,47,49],"2011":2,"2018":49,"2019":49,"2d":[19,42,46],"3":[41,42,49],"3d":[3,19,20,33,41,42,45,46,49],"3dunet":[42,46],"4":[39,47],"40":[41,46],"5":[41,47],"64":[41,42,46],"64x64x64":42,"65":46,"868688":20,"90":41,"break":48,"case":[41,45,47],"class":[1,2,3,4,5,6,7,8,10,11,12,13,16,17,19,20,21,22,23,25,26,27,28,29,30,31,32,33,34,35,36,37,40,42,47],"default":[41,42,43,47,49],"do":[14,41,42,47,49],"final":46,"function":[1,2,3,16,17,36,37,46,49],"import":[40,43],"kr\u00e4henb\u00fchl":2,"new":[34,40,41,45],"switch":[41,47],"true":48,"try":[41,46,49],"while":[41,43,46],A:[42,45,46,47,49],As:42,At:[42,46],By:41,For:[12,39,40,41,42,43,47,48,49],If:[39,41,42,43,44,45,46,47,49],In:[41,42,43],It:[6,41,42,45,46,47],No:49,Not:41,OR:[43,47],Or:41,The:[1,2,19,20,41,42,43,44,45,46,47,48,49],Then:[41,49],These:49,To:[39,40,41,42,44,45,46,49],With:[39,41],_:42,__init__:40,_pred:42,ab:[2,19,20,49],abc:40,about:[29,49],abov:[39,41,42,46],abstractmethod:40,access:[39,41,45,49],accord:[43,46,47,49],account:46,achard:49,achiev:41,across:41,action:0,activ:43,actual:1,ad:[40,41,46,47],adapt:[9,20,47,49],adaptivemotorcontrollab:43,add:[0,40,43],addit:[39,47],addition:[41,42,45],adjust:[39,41,42,46,47,49],advanc:[41,42,49],after:[41,43,46,47,49],afterward:48,again:[14,39,41,46],against:47,ai:46,al:49,algorithm:[42,46,49],alias:36,align:41,all:[0,24,35,41,42,43,46,49],allow:[39,42,45,46],alongsid:42,alpha:2,alreadi:[41,45],also:[2,39,41,42,45,46,47,49],altern:46,alwai:[41,42,45],among:47,amount:47,an:[39,40,41,42,43,45,46,47],analysi:48,analyz:41,ani:[41,42,43,46],anisotrop:[39,41,42,45],anisotropi:[39,42,45,48],annot:[41,45,49],anoth:39,answer:47,anytim:41,anywher:45,api:[46,48],appear:[2,39,42,44],append:45,appli:49,applic:42,appropri:[41,42],approxim:20,ar:[1,6,39,41,42,44,45,46,47,48,49],archiv:41,area:41,around:[39,47],arrai:2,artifact:[41,47,48],arxiv:[2,19,20,49],ascend:41,assess:46,assign:[41,48],assist:49,associ:41,assum:[41,44],attempt:42,attribut:[3,21,40],augment:[41,46],auto:41,autoencod:[42,46],autom:49,automat:[14,41,42,44,46,47],autosav:46,avail:[2,42,46,49],avoid:[41,42],awar:46,back:41,backend:[43,49],background:[42,47],backward:47,base:[12,19,20,25,41,42,46,48,49],basic:4,batch:[40,41,46],bce:47,becom:46,been:[41,45,49],befor:[39,41,45,46],begin:[41,42,44,45,46],behavior:41,being:[45,47],below:[41,42,43,44,46,48,49],beneath:48,best:[41,42,44],beta:2,better:[0,41,45,46,47],between:[41,42,44,46,47],bias:46,bibliographi:0,big:41,bilater:2,binar:[42,46],binari:[47,48],block:[15,18],blue:44,border:42,both:[43,46],bottom:[39,42,48],bound:47,box:[6,40],brain:[41,42,46,49],brainreg:49,bright:[47,49],build:[15,18,41],button:[39,41,42,44,45,46,49],c:2,calcul:41,can:[39,41,42,44,45,46,47,48,49],cannot:49,cap:44,capabl:[43,46,49],captur:41,caus:[41,42],cd:43,cell:[41,42,46,49],cellseg3d:[41,45,46],center:[41,49],central:35,centroid:[41,42,48],certain:[47,48,49],chang:[39,41,47],channel:40,check:[39,41,42,45,48],checkbox:39,choic:41,choos:[39,41,42,45,47,49],chose:41,chosen:[42,46],chunk:42,clear:[41,49],click:[39,41,45,46],clone:[43,49],close:[41,45,46,47],closer:47,clume:48,clump:48,cluster:47,cnn:41,code:[1,5,24],code_model:[42,46],code_plugin:[39,42,45,46,48],coeffici:44,colab:47,collabor:49,collect:41,color:[2,41],colormap:[39,42],com:[43,48],come:49,command:[43,46,48],comparison:[44,46],compat:[1,41,42,43,46,49],compens:41,complet:[41,46],compon:[41,42,48],compris:46,comput:[20,41,42,44,47,48,49],conda:43,conduct:46,confid:42,connect:[2,41,42,46,48],consid:[39,47],consist:[41,46],constraint:42,consult:[41,43],consumpt:46,contain:[1,2,5,21,22,24,42,45,46,47],context:45,continu:45,contrast:[39,42,49],contribut:49,control:[39,41,46,49],converg:[46,47],convert:[41,42,49],convolut:[42,46],coordin:[41,42,48],copi:[41,45,46],correct:[39,41,45,49],correspond:[41,45],cortex:41,cortic:41,cost:[20,47],costli:41,could:[41,46],counter:41,cpu:[41,42,43,46],creat:[43,45,46],credit:49,crf:[1,27],criteria:43,critic:47,crop:[28,49],cross:47,crossentropi:46,crucial:46,csv:[41,42,45,48],csv_cell_plot:41,ctrl:[39,41],cube:[46,48],cubic:[41,46],cuda:[43,46,49],current:[0,9,30,39,40,41,42,45,46,48],curv:41,custom:[6,21,41,42,43,46,47,49],cut:20,cyril:49,d:[2,39,41],data:[39,41,42,45,47,49],dataset:[41,42,45,46,47],date:42,deceler:41,decent:41,decid:[41,45,46],decod:[12,47],decreas:[41,47],dedic:49,deep:[41,42,46,47,49],def:40,defin:[39,42,44,46],deform:46,degre:49,delet:14,demo:49,dens:42,depend:[39,43,46,47,48,49],deriv:42,descend:41,describ:[39,47],design:41,desir:[39,41,42],detail:[42,49],detect:[46,49],determin:[41,44,46],determinist:[41,46],develop:49,deviat:[2,47],devic:42,diagram:[41,48],dialog:45,diamet:41,dice:[41,44,46],dictat:[41,47],did:41,differ:[42,47],dim:40,dimens:[39,42,46],directli:[39,42,43,47],directori:[41,48],disabl:[42,47],displai:[41,42,44,46],distinct:41,distinguish:47,distribut:47,divid:42,doc:41,document:[20,29],doe:[47,48],doi:49,domin:42,don:43,done:[39,46,47],down:48,download:[14,40,46],dr:49,dropdown:39,durat:39,dure:[41,43,46,47],dynam:39,e:[41,42,43,49],each:[2,41,42,44,45,46,48],easi:41,easier:[41,45],edg:[2,41],effect:42,effici:[2,41,45],egg:48,either:[41,42,43,46,47],elast:46,elimin:48,emphas:41,empti:39,enabl:[39,41,42,45,46],encount:43,enhanc:[42,46],ensur:[1,40,41,42,44,46,47],enter:[41,48],entir:[42,46],entropi:47,env:43,environ:[43,49],epoch:[41,46,47],equal:[41,46],error:[40,43,47,49],especi:49,et:49,etc:46,evalu:46,even:41,everi:[41,46],exact:41,examin:49,exampl:[39,41,46,48],execut:46,exist:[41,45],experi:42,explain:41,explod:47,extend:[41,46],extens:[41,42],extract:[41,46],eyer:[2,48],f:43,factor:[46,47],faster:[20,42],featur:[41,47],feel:[14,43,49],few:[42,47],file:[39,40,41,42,44,45,46,48],file_ext:42,fill:[42,48],filter:41,find:[41,42,44,45,46,47,48,49],finish:[41,42],first:[39,42,47,49],fit:41,fix:[39,42],fkodom:20,flexibl:41,flip:[44,46],fmri:41,focal:41,focus:47,folder:[1,24,39,40,41,42,43,44,45,46,48,49],follow:[2,40,42,45,46,49],foreground:42,format:[39,42,45,46],forward:40,found:48,frac:[41,44],fraction:[42,48],fragment:46,framework:[1,4],free:[14,43,49],frequent:[41,46],from:[2,19,39,41,42,43,44,46,47,49],full:39,full_plot:41,fulli:[2,6,42,46,47,49],fund:49,further:[39,49],fuse:48,futur:[6,46],g:[41,42],gain:39,gamma:2,gaussian:2,gener:[41,42,45,46,47,49],get:[0,40,41,43,49],gh:0,git:[43,48],github:[42,43,46,47,48,49],given:[41,46,48],global:[42,48],go:[39,49],goe:40,good:[41,42,47],gpu:[42,43,46,49],gradient:41,graph:45,greatli:[41,47,49],grid:42,ground:44,guarante:[41,49],guid:[42,48,49],guidelin:41,h:2,ha:[42,44,47,49],haas:49,halo:47,halt:41,hand:41,happen:41,har:41,hardwar:[43,49],have:[39,41,42,43,44,45,46,47,48,49],help:[40,49],her:49,here:[6,41,46,47,48,49],hesit:47,high:41,higher:46,highli:43,highlight:[39,44],histogram:49,hit:[39,42],host:14,hous:49,hover:49,how:[6,41,42,46],howev:[41,46],http:[2,19,20,43,46,48,49],human:41,i:41,id:[41,42,48],ideal:[41,46,47],ident:45,identifi:41,ieee:20,ieeexplor:20,ignor:48,imag:[2,3,19,20,26,39,42,43,44,45,46,47,49],imageri:41,impact:41,implement:[2,6,19,20,41,42,46,49],improv:[39,41,46,47],in_channel:40,inaccuraci:44,includ:[40,42,49],incorpor:41,increas:[46,47],indic:41,individu:42,infer:[1,2,4,12,21,23,31,43,46,47,49],inferencework:21,info:49,inform:46,initi:[41,46,49],input:[2,39,41,42,46,48],input_image_s:40,inspect:45,inspir:[2,47],instal:[41,46,48],instanc:[1,3,41,42,46,49],instance_segment:1,instead:[39,41],instruct:[41,42,43,49],integ:48,integr:41,intend:41,intens:[46,47],intensity_sigma:47,interest:[39,48],interrupt:46,interv:[41,46],io:49,ipynb:41,isnt:39,issu:[40,41,43],its:[41,43,47],itself:41,job:[21,42],json:40,jupyt:47,k:2,keep:[41,42,45],kei:46,kernel:2,koltun:2,kousi:49,kuli:49,kwarg:40,label:[33,39,42,44,45,46,49],laboratori:49,larg:[41,44,46,47],larger:[41,46,48],later:42,latter:41,launch:[41,42],layer:[41,42,45,48],layout:[39,41,42,45,46],lead:[40,44,46],learn:[46,47],least:46,leav:[41,42],left:[39,41],legaci:9,length:41,less:[41,47],lesser:49,let:[39,46],leverag:49,librari:[0,2,41,49],light:49,lightweight:41,ligthsheet:41,like:[39,40,46],limit:[39,42],link:[29,42,43,46],linux:[43,49],list:[42,46,48],ll:41,load:[41,42,46],local:[43,47,49],locat:[39,41,45,46],log:[42,45,46],login:46,longer:41,loop:41,loss:[20,41,46,47],low:[41,44],lower:[41,46,47],lucasb:[2,48],m1:49,m2:49,macbook:43,machin:46,mackenzi:49,maco:[43,49],magnitud:47,mai:[39,42,45,46,47,48],main:49,mainli:49,maintain:41,make:[39,41,42,45,47],manag:45,mandatori:43,mani:[46,47,49],manipul:41,manual:[42,45,49],map:[41,47,48],mark:44,master:48,match:[41,43,44],mathi:49,matter:41,maxim:49,maximum:41,mean:[41,47],measur:44,medic:[41,42,46],memori:[20,41,42,46],menu:[39,48],mesospim:[41,49],method:[3,41,42,47,48],metric:[42,46,48],mice:49,micron:[39,42],microscop:[39,41,48,49],microscopi:49,might:[6,41,42,44,46,47,49],miniconda3:43,minim:47,miss:49,modal:42,mode:42,model:[1,22,45,47,49],model_dict:40,model_framework:[1,40],model_templ:40,modeltemplate_:40,modifi:[39,40,41],modul:[0,1,3,5,15,18,21,24,39,41,42,45,46,47,49],moment:[45,46],monai:[41,43,46,49],monitor:[41,45],more:[39,41,42,46,47,49],most:41,mostli:15,motor:49,mous:41,move:39,mri:[42,46],mse:47,much:46,multipl:[39,41,45],multipli:47,must:[40,47],n:[2,20],name:[39,40,41,44,45,46,48],napari:[4,39,41,42,43,45,46],napari_cellseg3d:[39,40,42,45,46,48],napari_cellseg3d_m1:43,navig:[39,43],ncut:47,nearest:41,necessari:[40,45,46],need:[14,39,40,41,46,49],neg:41,net:[2,12,19,49],network:[42,46],neural:[41,42,46],neuron:41,next:39,nip:2,normal:47,notabl:42,note:[6,41,42,43,46,49],notebook:[42,47,48],notic:47,now:[40,42,46],nuclei:[41,49],number:[41,42,44,45,46,47,48],numer:[44,46],o:41,object:[42,47,49],occupi:41,offer:41,often:[41,48],onc:[39,41,42,45,46,47],one:[39,41,45,47],ones:42,onli:[12,40,41,42,46,48],opac:39,open:[34,41,43,45,47,49],opt:41,optim:[41,46,48],optimis:[41,47],option:[39,41,42,43,45,47,49],order:[39,47],org:[2,19,20,49],orient:44,origin:[41,42,46,47,48,49],original_nam:42,os:43,other:42,otherwis:42,otsu:[41,42,48,49],our:[41,42,43,46,47,49],out:[6,40,41,42],out_channel:40,outlier:47,outlin:43,output:[40,41,42,46],outsid:49,over:[39,41,49],overal:41,overlap:42,own:[41,42,49],packag:[43,46,48,49],pad:[41,44,46],page:[29,43,46,48,49],pair:[44,48],paper:[42,46,47],paramet:[2,39,41,42,46,48],part:[2,41,46],partial:46,particularli:43,pass:[40,47],patch:[41,46],path:[41,45,46],patienc:46,paus:41,per:45,percentag:41,perfect:44,perform:[19,41,42,46,47],philipp:2,pip:[43,46,48,49],pixel:[2,41,42,46,47,48],place:40,plane:45,plateau:[46,47],platform:46,pleas:[6,14,40,41,42,43,44,46,47,48,49],plot:[41,44,45,46,48],plugin:[1,4,6,9,24,25,27,28,29,31,32,33,35,39,41,42,43,47,48],plugin_bas:[39,44,45],plugin_convert:48,plugin_crf:48,plugin_crop:39,plugin_metr:44,plugin_model_infer:42,plugin_model_train:46,plugin_review:45,plugin_review_dock:45,poor:47,popul:42,port:49,portion:39,posit:[39,42,47],possibl:46,post:2,postprocess:1,potenti:[2,41,46],power:[41,44,46],pre:[41,42,46,49],precis:47,predict:[2,41,44,45,48,49],prefer:[41,46],prepar:41,present:[41,42,46],press:[39,41,44,45,46],pretrain:47,pretrained_model:40,previou:41,primari:41,probabl:[2,41],process:[2,26,41,46,48,49],produc:[39,41,42],program:46,progress:[40,41,42,45,47],project:[41,42,45,46,49],propag:46,properti:49,proport:[41,46],propos:20,provid:[41,42,45,46,47,49],proxim:47,pth:[40,41],purpos:[13,48],py:[1,40],pyclesperanto:49,pydens:2,pydensecrf:[2,48],pyqt5:49,pyside2:49,python:46,pytorch:[10,40,41,42,46,49],qt:[43,49],qualiti:[41,48],quantiti:42,quick:[41,49],quicker:46,quickli:47,quicksav:[39,41],radiu:47,rais:47,ram:42,ran:42,random:46,randomli:44,rang:[39,44,48],rate:[41,46,47],rather:42,ratio:[41,42,48],raw:46,re:[41,42,46,49],reach:[41,47],reader:[43,49],readi:[41,42,45,46],recap:45,recommend:[41,42,43,46,47,49],reconstruct:47,record:[41,46],red:44,reduc:[20,41,42,46],refer:[42,43,46,47,48],refin:[48,49],regard:49,region:[39,41,47,49],regionprop:49,registr:49,regular:[42,46],reimplement:[10,40,41,47],relat:[23,24,43,49],relev:39,reli:47,remain:39,remap:47,rememb:41,remov:[12,41,45],repeat:41,replac:[39,40],repositori:[41,43],repres:41,reproduc:[41,46],request:46,requir:[2,41,42,43,46,47],requisit:49,research:2,reset:39,resiz:[39,45],resolut:[39,41,42,48],restart:[39,41],result:[41,44,45,46,47,48],retain:41,retrain:[42,47],review:[33,34,39,49],rich:41,right:[39,41],robert:49,robust:47,rotat:44,roughli:41,round:48,run:[21,41,42,43,48,49],s41592:49,s:[39,41,43,45,46,48,49],sa:2,same:[39,41,42,45,46,47],sampl:[46,49],satisfactori:47,satisfi:41,save:[41,42,45,46,48],sb:2,scale:[2,39,45,47],schedul:46,score:44,scratch:41,search:43,second:39,section:[41,42,43,46,49],see:[39,41,42,43,46,48,49],seed:[41,46],seem:42,segment:[1,3,19,20,41,42,46,47,49],segresnet:[7,41,42,46],select:[39,41,42,43,45,46,48],self:40,semant:[41,42,46,49],sensit:47,separ:[41,42,46,49],seper:41,sequenti:45,session:[34,39,41,45],set:[39,42,44,46,47],setup:[0,49],sever:[23,26,42,46,49],sg:2,shape:2,sheet:49,shift:[41,45,46],shortcut:41,should:[41,42,44,45,46,47,49],show:[6,29,41,42],shown:[42,46],sigma:[41,47],significantli:47,similar:[41,44,47],similarli:42,simpl:48,simpli:[39,41,42,46,49],simultan:[39,41,46],singl:[41,45,46],site:46,size:[39,41,42,44,46,48],skimag:49,slice:[41,45],slider:[39,41,42],small:[41,44],smaller:[39,41,42,44,48],smooth:2,so:[41,45],soft:20,softncut:47,softwar:49,solut:43,some:41,sort:44,sourc:[43,49],spatial:[2,47],specif:[39,41,42,43],specifi:[40,41,42,46,48],speed:46,spent:41,spheric:[41,42,48],squar:47,stabil:47,stack:[42,45,46],standard:[2,47],start:[34,39,41,42,43,45,46],stat:[41,42],state:41,statist:42,statu:[41,45],step:[2,41,43,46,47],stephan:49,stick:41,still:[39,40,41],stop:[41,46],store:[41,46],strongli:49,structur:40,substanti:41,succe:42,success:[43,49],suffici:44,suggest:46,suit:41,sum:47,superior:41,supervis:[47,49],support:[6,40,41,42,45,46,49],sure:[41,42,45],surround:41,swin:[42,46],swinunetr:[8,41,42,46],system:[41,45,46],t:43,tab:[41,47],tabl:46,take:47,taken:[41,45],task:49,templat:6,ten:47,tensor:40,term:47,termin:43,test:13,text:41,than:[41,42,48],thank:49,thei:[14,41,44,45,46,49],them:[14,41,42,45,46,48,49],theori:41,thi:[1,6,20,24,39,40,41,42,43,44,45,46,47,48,49],those:47,three:39,threshold:[39,41,42,44],through:46,tif:[41,42,45,46],tiff:46,time:[39,41,42,45,46,47],timokleia:49,tini:29,tissu:[41,49],todo:0,too:41,tool:[39,41,44,48,49],toolbox:49,tooltip:49,topograph:48,topographi:48,torch:[40,49],total:[41,42,48],touch:48,track:[41,42,45,46],trailmap:[9,10,15,41,42,46,49],trailmap_m:[42,46],train:[1,4,12,22,23,32,42,43,48,49],transfer:[41,46],transform:[42,46,48],truth:44,tumor:[42,46],tutori:[0,41],tverski:46,two:[41,44,46,47],under:[41,46],underneath:46,understand:[45,49],unetr:46,uniform:[41,46],uninstal:43,uniqu:[41,48],unless:41,unlik:47,unstabl:47,unsupervis:[19,20,41,47,49],unsur:41,unus:30,up:46,upcom:46,updat:[0,39,42,45],url:40,us:[1,2,6,9,12,15,22,39,41,42,43,44,45,46,47,48],usabl:41,usag:[41,46],user:[36,43,46,49],util:[23,26,28,35,39,42,45,46,49],valid:[41,46],valu:[41,42,46,47,48],vari:[41,44],variabl:[37,41],varianc:46,varieti:41,variou:[42,49],ve:41,veri:[41,49],verif:44,verifi:45,version:[0,9,19,20,46,47,49],versu:[41,46],via:[43,46,49],vidal:49,view:[41,42],viewer:[39,44,46],visibl:[39,42],visual:[45,49],visualis:41,vladlen:2,vnet:[11,41,42,46],voigt:49,volum:[33,41,42,45,46,49],volume_:41,volumetr:[42,46],voronoi:[41,42,48,49],vram:42,w1:2,w2:2,w:[2,12,19,49],wa:[20,42,47,49],wai:[0,39],wait:[46,47],want:[39,41,42,45],watch:47,watersh:[41,42,48],we:[40,41,43,46,49],websit:[43,46,49],weight:[2,12,14,40,41,42,46,47,49],weights_fil:40,well:[40,46,48,49],were:49,what:[41,49],when:[34,39,41,42,44,46,47],whenev:46,where:[41,42,45],wherea:41,whether:[42,44,45,49],which:[1,21,39,41,45,46,47],whole:[41,47,49],whose:41,widget:34,window:[41,42,43,45,48,49],wip:[40,49],wish:[41,42,49],within:[39,41,42,45,46,47],without:[41,42,43,49],wnet:[0,41,46,49],work:[39,40,41,45,46,48],worker:[1,21,22,23],worker_infer:[1,42],worker_train:[1,46],worker_util:1,workflow:[41,49],would:40,wrapper:[1,5,7,8,11,12],written:42,wrong:44,wyss:49,x:[39,40,41,42,44,45,48],xia:49,y:[39,40,41,42,44,45,48],yet:[6,41],yield:41,yml:43,you:[14,39,40,41,42,43,44,45,46,47,48,49],your:[40,41,42,43,44,45,46,47,48,49],z:[39,40,41,42,45,48],zerocostdl4m:47,zip:[41,46],zoom:39},titles:["<no title>","napari_cellseg3d.code_models","napari_cellseg3d.code_models.crf","napari_cellseg3d.code_models.instance_segmentation","napari_cellseg3d.code_models.model_framework","napari_cellseg3d.code_models.models","napari_cellseg3d.code_models.models.TEMPLATE_model","napari_cellseg3d.code_models.models.model_SegResNet","napari_cellseg3d.code_models.models.model_SwinUNetR","napari_cellseg3d.code_models.models.model_TRAILMAP","napari_cellseg3d.code_models.models.model_TRAILMAP_MS","napari_cellseg3d.code_models.models.model_VNet","napari_cellseg3d.code_models.models.model_WNet","napari_cellseg3d.code_models.models.model_test","napari_cellseg3d.code_models.models.pretrained","napari_cellseg3d.code_models.models.unet","napari_cellseg3d.code_models.models.unet.buildingblocks","napari_cellseg3d.code_models.models.unet.model","napari_cellseg3d.code_models.models.wnet","napari_cellseg3d.code_models.models.wnet.model","napari_cellseg3d.code_models.models.wnet.soft_Ncuts","napari_cellseg3d.code_models.worker_inference","napari_cellseg3d.code_models.worker_training","napari_cellseg3d.code_models.workers_utils","napari_cellseg3d.code_plugins","napari_cellseg3d.code_plugins.plugin_base","napari_cellseg3d.code_plugins.plugin_convert","napari_cellseg3d.code_plugins.plugin_crf","napari_cellseg3d.code_plugins.plugin_crop","napari_cellseg3d.code_plugins.plugin_helper","napari_cellseg3d.code_plugins.plugin_metrics","napari_cellseg3d.code_plugins.plugin_model_inference","napari_cellseg3d.code_plugins.plugin_model_training","napari_cellseg3d.code_plugins.plugin_review","napari_cellseg3d.code_plugins.plugin_review_dock","napari_cellseg3d.code_plugins.plugin_utilities","napari_cellseg3d.interface","napari_cellseg3d.utils","API reference","Cropping\u2702\ufe0f","Advanced : Custom models","Detailed walkthrough - Supervised learning","Inference\ud83d\udcca","Installation guide \u2699","Metrics utility guide \ud83d\udcc8","Review\ud83d\udd0d","Training\ud83d\udcc9","Advanced : WNet training","Utilities \ud83d\udee0","Welcome to CellSeg3D!"],titleterms:{"1":[46,48],"10":48,"2":[46,48],"3":[46,48],"3d":48,"4":48,"5":48,"6":48,"7":48,"8":48,"9":48,"function":[39,42,45],"new":39,For:46,acknowledg:49,action:48,advanc:[40,46,47],analysi:41,anisotrop:48,api:38,arm64:43,avail:48,buildingblock:16,cellseg3d:[43,49],clear:48,code:[39,42,44,45,46,48],code_model:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23],code_plugin:[24,25,26,27,28,29,30,31,32,33,34,35],common:47,condit:48,content:49,convers:41,convert:48,creat:39,crf:[2,48],crop:[39,41,48],custom:40,data:46,detail:41,detect:41,document:49,field:48,fragment:48,guid:[41,43,44],imag:[41,48],infer:[41,42],instal:[43,49],instanc:48,instance_segment:3,integr:46,interfac:[36,39,42,45],issu:47,jupyt:41,label:[41,48],larg:48,launch:[39,45],layer:39,learn:41,m1:43,m2:43,mac:43,metric:44,model:[5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,40,41,42,46],model_framework:4,model_segresnet:7,model_swinunetr:8,model_test:13,model_trailmap:9,model_trailmap_m:10,model_vnet:11,model_wnet:12,napari:49,napari_cellseg3d:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37],notebook:41,object:[41,48],option:46,other:49,paramet:[44,47],plot:42,plugin:49,plugin_bas:25,plugin_convert:26,plugin_crf:27,plugin_crop:28,plugin_help:29,plugin_metr:30,plugin_model_infer:31,plugin_model_train:32,plugin_review:33,plugin_review_dock:34,plugin_util:35,pre:43,pretrain:14,process:[39,45],pyqt5:43,pyside2:43,pytorch:43,random:48,refer:[38,49],remov:48,requir:[44,49],requisit:43,resiz:48,result:42,review:[41,45],run:46,save:39,score:41,semant:48,set:41,small:48,soft_ncut:20,sourc:[39,42,44,45,46,48],statist:48,supervis:[41,46],tab:46,template_model:6,threshold:48,train:[41,46,47],troubleshoot:47,unet:[15,16,17],unsupervis:[42,46],up:41,us:49,usag:49,util:[37,41,44,48],volum:[39,48],walkthrough:41,wandb:46,welcom:49,wnet:[18,19,20,42,47],worker_infer:21,worker_train:22,workers_util:23,your:39}}) \ No newline at end of file +Search.setIndex({docnames:["TODO","source/code/_autosummary/napari_cellseg3d.code_models","source/code/_autosummary/napari_cellseg3d.code_models.crf","source/code/_autosummary/napari_cellseg3d.code_models.instance_segmentation","source/code/_autosummary/napari_cellseg3d.code_models.model_framework","source/code/_autosummary/napari_cellseg3d.code_models.models","source/code/_autosummary/napari_cellseg3d.code_models.models.TEMPLATE_model","source/code/_autosummary/napari_cellseg3d.code_models.models.model_SegResNet","source/code/_autosummary/napari_cellseg3d.code_models.models.model_SwinUNetR","source/code/_autosummary/napari_cellseg3d.code_models.models.model_TRAILMAP","source/code/_autosummary/napari_cellseg3d.code_models.models.model_TRAILMAP_MS","source/code/_autosummary/napari_cellseg3d.code_models.models.model_VNet","source/code/_autosummary/napari_cellseg3d.code_models.models.model_WNet","source/code/_autosummary/napari_cellseg3d.code_models.models.model_test","source/code/_autosummary/napari_cellseg3d.code_models.models.pretrained","source/code/_autosummary/napari_cellseg3d.code_models.models.unet","source/code/_autosummary/napari_cellseg3d.code_models.models.unet.buildingblocks","source/code/_autosummary/napari_cellseg3d.code_models.models.unet.model","source/code/_autosummary/napari_cellseg3d.code_models.models.wnet","source/code/_autosummary/napari_cellseg3d.code_models.models.wnet.model","source/code/_autosummary/napari_cellseg3d.code_models.models.wnet.soft_Ncuts","source/code/_autosummary/napari_cellseg3d.code_models.worker_inference","source/code/_autosummary/napari_cellseg3d.code_models.worker_training","source/code/_autosummary/napari_cellseg3d.code_models.workers_utils","source/code/_autosummary/napari_cellseg3d.code_plugins","source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_base","source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_convert","source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_crf","source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_crop","source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_helper","source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_metrics","source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_model_inference","source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_model_training","source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_review","source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_review_dock","source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_utilities","source/code/_autosummary/napari_cellseg3d.interface","source/code/_autosummary/napari_cellseg3d.utils","source/code/api","source/guides/cropping_module_guide","source/guides/custom_model_template","source/guides/detailed_walkthrough","source/guides/inference_module_guide","source/guides/installation_guide","source/guides/metrics_module_guide","source/guides/review_module_guide","source/guides/training_module_guide","source/guides/training_wnet","source/guides/utils_module_guide","welcome"],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,"sphinxcontrib.bibtex":9,sphinx:56},filenames:["TODO.md","source/code/_autosummary/napari_cellseg3d.code_models.rst","source/code/_autosummary/napari_cellseg3d.code_models.crf.rst","source/code/_autosummary/napari_cellseg3d.code_models.instance_segmentation.rst","source/code/_autosummary/napari_cellseg3d.code_models.model_framework.rst","source/code/_autosummary/napari_cellseg3d.code_models.models.rst","source/code/_autosummary/napari_cellseg3d.code_models.models.TEMPLATE_model.rst","source/code/_autosummary/napari_cellseg3d.code_models.models.model_SegResNet.rst","source/code/_autosummary/napari_cellseg3d.code_models.models.model_SwinUNetR.rst","source/code/_autosummary/napari_cellseg3d.code_models.models.model_TRAILMAP.rst","source/code/_autosummary/napari_cellseg3d.code_models.models.model_TRAILMAP_MS.rst","source/code/_autosummary/napari_cellseg3d.code_models.models.model_VNet.rst","source/code/_autosummary/napari_cellseg3d.code_models.models.model_WNet.rst","source/code/_autosummary/napari_cellseg3d.code_models.models.model_test.rst","source/code/_autosummary/napari_cellseg3d.code_models.models.pretrained.rst","source/code/_autosummary/napari_cellseg3d.code_models.models.unet.rst","source/code/_autosummary/napari_cellseg3d.code_models.models.unet.buildingblocks.rst","source/code/_autosummary/napari_cellseg3d.code_models.models.unet.model.rst","source/code/_autosummary/napari_cellseg3d.code_models.models.wnet.rst","source/code/_autosummary/napari_cellseg3d.code_models.models.wnet.model.rst","source/code/_autosummary/napari_cellseg3d.code_models.models.wnet.soft_Ncuts.rst","source/code/_autosummary/napari_cellseg3d.code_models.worker_inference.rst","source/code/_autosummary/napari_cellseg3d.code_models.worker_training.rst","source/code/_autosummary/napari_cellseg3d.code_models.workers_utils.rst","source/code/_autosummary/napari_cellseg3d.code_plugins.rst","source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_base.rst","source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_convert.rst","source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_crf.rst","source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_crop.rst","source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_helper.rst","source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_metrics.rst","source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_model_inference.rst","source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_model_training.rst","source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_review.rst","source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_review_dock.rst","source/code/_autosummary/napari_cellseg3d.code_plugins.plugin_utilities.rst","source/code/_autosummary/napari_cellseg3d.interface.rst","source/code/_autosummary/napari_cellseg3d.utils.rst","source/code/api.rst","source/guides/cropping_module_guide.rst","source/guides/custom_model_template.rst","source/guides/detailed_walkthrough.rst","source/guides/inference_module_guide.rst","source/guides/installation_guide.rst","source/guides/metrics_module_guide.rst","source/guides/review_module_guide.rst","source/guides/training_module_guide.rst","source/guides/training_wnet.rst","source/guides/utils_module_guide.rst","welcome.rst"],objects:{"napari_cellseg3d.code_models":[[2,0,0,"-","crf"],[3,0,0,"-","instance_segmentation"],[4,0,0,"-","model_framework"],[5,0,0,"-","models"],[21,0,0,"-","worker_inference"],[22,0,0,"-","worker_training"],[23,0,0,"-","workers_utils"]],"napari_cellseg3d.code_models.models":[[6,0,0,"-","TEMPLATE_model"],[7,0,0,"-","model_SegResNet"],[8,0,0,"-","model_SwinUNetR"],[9,0,0,"-","model_TRAILMAP"],[10,0,0,"-","model_TRAILMAP_MS"],[11,0,0,"-","model_VNet"],[12,0,0,"-","model_WNet"],[13,0,0,"-","model_test"],[14,0,0,"-","pretrained"],[15,0,0,"-","unet"],[18,0,0,"-","wnet"]],"napari_cellseg3d.code_models.models.unet":[[16,0,0,"-","buildingblocks"],[17,0,0,"-","model"]],"napari_cellseg3d.code_models.models.wnet":[[19,0,0,"-","model"],[20,0,0,"-","soft_Ncuts"]],"napari_cellseg3d.code_plugins":[[25,0,0,"-","plugin_base"],[26,0,0,"-","plugin_convert"],[27,0,0,"-","plugin_crf"],[28,0,0,"-","plugin_crop"],[29,0,0,"-","plugin_helper"],[30,0,0,"-","plugin_metrics"],[31,0,0,"-","plugin_model_inference"],[32,0,0,"-","plugin_model_training"],[33,0,0,"-","plugin_review"],[34,0,0,"-","plugin_review_dock"],[35,0,0,"-","plugin_utilities"]],napari_cellseg3d:[[1,0,0,"-","code_models"],[24,0,0,"-","code_plugins"],[36,0,0,"-","interface"],[37,0,0,"-","utils"]]},objnames:{"0":["py","module","Python module"]},objtypes:{"0":"py:module"},terms:{"0":[41,42,44,47,48,49],"00915":2,"019":49,"0554":49,"08506":[2,19,20,49],"1":[39,40,41,42,44,47,49],"10":49,"100":[46,47],"1038":49,"120":41,"128":[41,46],"1606":2,"1711":[2,19,20,49],"1e":[41,47],"2":[39,41,42,43,44,47,49],"2011":2,"2018":49,"2019":49,"2d":[19,42,46],"3":[41,42,49],"3d":[3,19,20,33,41,42,45,46,49],"3dunet":[42,46],"4":[39,47],"40":[41,46],"5":[41,47],"64":[41,42,46],"64x64x64":42,"65":46,"868688":20,"90":41,"break":48,"case":[41,45,47],"class":[1,2,3,4,5,6,7,8,10,11,12,13,16,17,19,20,21,22,23,25,26,27,28,29,30,31,32,33,34,35,36,37,40,42,47],"default":[41,42,43,47,49],"do":[14,41,42,47,49],"final":46,"function":[1,2,3,16,17,36,37,43,46,49],"import":[40,43],"kr\u00e4henb\u00fchl":2,"new":[34,40,41,45],"switch":[41,47],"true":48,"try":[41,46,49],"while":[41,43,46],A:[42,45,46,47,49],As:42,At:[42,46],By:41,For:[12,39,40,41,42,43,47,48,49],If:[39,41,42,43,44,45,46,47,49],In:[41,42,43],It:[6,41,42,45,46,47],No:49,Not:41,OR:[43,47],Or:41,The:[1,2,19,20,41,42,43,44,45,46,47,48,49],Then:[41,49],These:49,To:[39,40,41,42,43,44,45,46,49],With:[39,41],_:42,__init__:40,_pred:42,ab:[2,19,20,49],abc:40,about:[29,49],abov:[39,41,42,46],abstractmethod:40,access:[39,41,45,49],accord:[43,46,47,49],account:46,achard:49,achiev:41,across:41,action:0,activ:43,actual:1,ad:[40,41,46,47],adapt:[9,20,47,49],adaptivemotorcontrollab:43,add:[0,40,43],addit:[39,43,47],addition:[41,42,45],adjust:[39,41,42,46,47,49],advanc:[41,42,49],after:[41,43,46,47,49],afterward:48,again:[14,39,41,46],against:47,ai:46,al:49,algorithm:[42,46,49],alias:36,align:41,all:[0,24,35,41,42,43,46,49],allow:[39,42,45,46],alongsid:42,alpha:2,alreadi:[41,45],also:[2,39,41,42,45,46,47,49],altern:46,alwai:[41,42,45],among:47,amount:47,an:[39,40,41,42,43,45,46,47],analysi:48,analyz:41,ani:[41,42,43,46],anisotrop:[39,41,42,45],anisotropi:[39,42,45,48],annot:[41,45,49],anoth:39,answer:47,anytim:41,anywher:45,api:[46,48],appear:[2,39,42,44],append:45,appli:49,applic:42,appropri:[41,42],approxim:20,ar:[1,6,39,41,42,43,44,45,46,47,48,49],archiv:41,area:41,around:[39,47],arrai:2,artifact:[41,47,48],arxiv:[2,19,20,49],ascend:41,assess:46,assign:[41,48],assist:49,associ:41,assum:[41,44],attempt:42,attribut:[3,21,40],augment:[41,46],auto:41,autoencod:[42,46],autom:49,automat:[14,41,42,44,46,47],autosav:46,avail:[2,42,43,46,49],avoid:[41,42],awar:46,back:41,backend:[43,49],background:[42,47],backward:47,base:[12,19,20,25,41,42,46,48,49],basic:4,batch:[40,41,46],bce:47,becom:46,been:[41,45,49],befor:[39,41,45,46],begin:[41,42,44,45,46],behavior:41,being:[45,47],below:[41,42,43,44,46,48,49],beneath:48,best:[41,42,44],beta:2,better:[0,41,45,46,47],between:[41,42,44,46,47],bias:[43,46],bibliographi:0,big:41,bilater:2,binar:[42,46],binari:[47,48],block:[15,18],blue:44,border:42,both:[43,46],bottom:[39,42,48],bound:47,box:[6,40],brain:[41,42,46,49],brainreg:49,bright:[47,49],build:[15,18,41,43],button:[39,41,42,44,45,46,49],c:2,calcul:41,can:[39,41,42,43,44,45,46,47,48,49],cannot:49,cap:44,capabl:[43,46,49],captur:41,caus:[41,42],cd:43,cell:[41,42,46,49],cellseg3d:[41,45,46],center:[41,49],central:35,centroid:[41,42,48],certain:[47,48,49],chang:[39,41,47],channel:40,check:[39,41,42,45,48],checkbox:39,choic:41,choos:[39,41,42,45,47,49],chose:41,chosen:[42,46],chunk:42,clear:[41,49],click:[39,41,45,46],clone:[43,49],close:[41,45,46,47],closer:47,clume:48,clump:48,cluster:47,cnn:41,code:[1,5,24],code_model:[42,46],code_plugin:[39,42,45,46,48],coeffici:44,colab:47,collabor:49,collect:41,color:[2,41],colormap:[39,42],com:[43,48],come:49,command:[43,46,48],comparison:[44,46],compat:[1,41,42,43,46,49],compens:41,complet:[41,46],compon:[41,42,48],compris:46,comput:[20,41,42,44,47,48,49],conda:43,conduct:46,confid:42,connect:[2,41,42,46,48],consid:[39,47],consist:[41,46],constraint:42,consult:[41,43],consumpt:46,contain:[1,2,5,21,22,24,42,45,46,47],context:45,continu:45,contrast:[39,42,49],contribut:49,control:[39,41,46,49],converg:[46,47],convert:[41,42,49],convolut:[42,46],coordin:[41,42,48],copi:[41,45,46],correct:[39,41,45,49],correspond:[41,45],cortex:41,cortic:41,cost:[20,47],costli:41,could:[41,46],counter:41,cpu:[41,42,43,46],creat:[43,45,46],credit:49,crf:[1,27,43],criteria:43,critic:47,crop:[28,49],cross:47,crossentropi:46,crucial:46,csv:[41,42,45,48],csv_cell_plot:41,ctrl:[39,41],cube:[46,48],cubic:[41,46],cuda:[43,46,49],current:[0,9,30,39,40,41,42,45,46,48],curv:41,custom:[6,21,41,42,43,46,47,49],cut:20,cyril:49,d:[2,39,41],data:[39,41,42,45,47,49],dataset:[41,42,45,46,47],date:42,deceler:41,decent:41,decid:[41,45,46],decod:[12,47],decreas:[41,47],dedic:49,deep:[41,42,46,47,49],def:40,defin:[39,42,44,46],deform:46,degre:49,delet:14,demo:49,dens:42,depend:[39,43,46,47,48,49],deriv:42,descend:41,describ:[39,47],design:41,desir:[39,41,42],detail:[42,49],detect:[46,49],determin:[41,44,46],determinist:[41,46],dev:43,develop:49,deviat:[2,47],devic:42,diagram:[41,48],dialog:45,diamet:41,dice:[41,44,46],dictat:[41,47],did:41,differ:[42,47],dim:40,dimens:[39,42,46],directli:[39,42,43,47],directori:[41,48],disabl:[42,47],displai:[41,42,44,46],distinct:41,distinguish:47,distribut:47,divid:42,doc:[41,43],document:[20,29,43],doe:[47,48],doi:49,domin:42,don:43,done:[39,46,47],down:48,download:[14,40,46],dr:49,dropdown:39,durat:39,dure:[41,43,46,47],dynam:39,e:[41,42,43,49],each:[2,41,42,44,45,46,48],easi:41,easier:[41,45],edg:[2,41],effect:42,effici:[2,41,45],egg:[43,48],either:[41,42,43,46,47],elast:46,elimin:48,emphas:41,empti:39,enabl:[39,41,42,45,46],encount:43,enhanc:[42,46],ensur:[1,40,41,42,44,46,47],enter:[41,48],entir:[42,46],entropi:47,env:43,environ:[43,49],epoch:[41,46,47],equal:[41,46],error:[40,43,47,49],especi:49,et:49,etc:46,evalu:46,even:41,everi:[41,46],exact:41,examin:49,exampl:[39,41,46,48],execut:46,exist:[41,45],experi:42,experiment:43,explain:41,explod:47,extend:[41,46],extens:[41,42],extract:[41,46],eyer:[2,43,48],f:43,factor:[46,47],faster:[20,42],featur:[41,47],feel:[14,43,49],few:[42,47],file:[39,40,41,42,44,45,46,48],file_ext:42,fill:[42,48],filter:41,find:[41,42,44,45,46,47,48,49],finish:[41,42],first:[39,42,47,49],fit:41,fix:[39,42],fkodom:20,flexibl:41,flip:[44,46],fmri:41,focal:41,focus:47,folder:[1,24,39,40,41,42,43,44,45,46,48,49],follow:[2,40,42,43,45,46,49],foreground:42,format:[39,42,45,46],forward:40,found:48,frac:[41,44],fraction:[42,48],fragment:46,framework:[1,4],free:[14,43,49],frequent:[41,46],from:[2,19,39,41,42,43,44,46,47,49],full:39,full_plot:41,fulli:[2,6,42,46,47,49],fund:49,further:[39,49],fuse:48,futur:[6,46],g:[41,42],gain:39,gamma:2,gaussian:2,gener:[41,42,45,46,47,49],get:[0,40,41,43,49],gh:0,git:[43,48],github:[42,43,46,47,48,49],given:[41,46,48],global:[42,48],go:[39,49],goe:40,good:[41,42,47],gpu:[42,43,46,49],gradient:41,graph:45,greatli:[41,47,49],grid:42,ground:44,guarante:[41,49],guid:[42,48,49],guidelin:41,h:2,ha:[42,44,47,49],haas:49,halo:47,halt:41,hand:41,happen:41,har:41,hardwar:[43,49],have:[39,41,42,43,44,45,46,47,48,49],help:[40,49],her:49,here:[6,41,46,47,48,49],hesit:47,high:41,higher:46,highli:43,highlight:[39,44],histogram:49,hit:[39,42],host:14,hous:49,hover:49,how:[6,41,42,46],howev:[41,46],http:[2,19,20,43,46,48,49],human:41,i:41,id:[41,42,48],ideal:[41,46,47],ident:45,identifi:41,ieee:20,ieeexplor:20,ignor:48,imag:[2,3,19,20,26,39,42,43,44,45,46,47,49],imageri:41,impact:41,implement:[2,6,19,20,41,42,46,49],improv:[39,41,46,47],in_channel:40,inaccuraci:44,includ:[40,42,49],incorpor:41,increas:[46,47],indic:41,individu:42,infer:[1,2,4,12,21,23,31,43,46,47,49],inferencework:21,info:49,inform:46,initi:[41,46,49],input:[2,39,41,42,46,48],input_image_s:40,inspect:45,inspir:[2,47],instal:[41,46,48],instanc:[1,3,41,42,46,49],instance_segment:1,instead:[39,41],instruct:[41,42,43,49],integ:48,integr:[41,43],intend:41,intens:[46,47],intensity_sigma:47,interest:[39,48],interrupt:46,interv:[41,46],io:49,ipynb:41,isnt:39,issu:[40,41,43],its:[41,43,47],itself:41,job:[21,42],json:40,jupyt:47,k:2,keep:[41,42,45],kei:46,kernel:2,koltun:2,kousi:49,kuli:49,kwarg:40,label:[33,39,42,44,45,46,49],laboratori:49,larg:[41,44,46,47],larger:[41,46,48],later:42,latter:41,launch:[41,42],layer:[41,42,45,48],layout:[39,41,42,45,46],lead:[40,44,46],learn:[46,47],least:46,leav:[41,42],left:[39,41],legaci:9,length:41,less:[41,47],lesser:49,let:[39,46],leverag:49,librari:[0,2,41,49],light:49,lightweight:41,ligthsheet:41,like:[39,40,46],limit:[39,42],link:[29,42,43,46],linux:[43,49],list:[42,46,48],ll:41,load:[41,42,46],local:[43,47,49],locat:[39,41,45,46],log:[42,45,46],login:46,longer:41,loop:41,loss:[20,41,46,47],low:[41,44],lower:[41,46,47],lucasb:[2,43,48],m1:49,m2:49,macbook:43,machin:46,mackenzi:49,maco:[43,49],magnitud:47,mai:[39,42,45,46,47,48],main:49,mainli:49,maintain:41,make:[39,41,42,45,47],manag:45,mandatori:43,mani:[46,47,49],manipul:41,manual:[42,45,49],map:[41,47,48],mark:44,master:[43,48],match:[41,43,44],mathi:49,matter:41,maxim:49,maximum:41,mean:[41,47],measur:44,medic:[41,42,46],memori:[20,41,42,46],menu:[39,48],mesospim:[41,49],method:[3,41,42,47,48],metric:[42,46,48],mice:49,micron:[39,42],microscop:[39,41,48,49],microscopi:49,might:[6,41,42,44,46,47,49],miniconda3:43,minim:47,miss:49,modal:42,mode:42,model:[1,22,43,45,47,49],model_dict:40,model_framework:[1,40],model_templ:40,modeltemplate_:40,modifi:[39,40,41],modul:[0,1,3,5,15,18,21,24,39,41,42,45,46,47,49],moment:[45,46],monai:[41,43,46,49],monitor:[41,45],more:[39,41,42,46,47,49],most:41,mostli:15,motor:49,mous:41,move:39,mri:[42,46],mse:47,much:46,multipl:[39,41,45],multipli:47,must:[40,47],n:[2,20],name:[39,40,41,44,45,46,48],napari:[4,39,41,42,43,45,46],napari_cellseg3d:[39,40,42,45,46,48],napari_cellseg3d_m1:43,navig:[39,43],ncut:47,nearest:41,necessari:[40,45,46],need:[14,39,40,41,46,49],neg:41,net:[2,12,19,49],network:[42,46],neural:[41,42,46],neuron:41,next:39,nip:2,normal:47,notabl:42,note:[6,41,42,43,46,49],notebook:[42,47,48],notic:47,now:[40,42,46],nuclei:[41,49],number:[41,42,44,45,46,47,48],numer:[44,46],o:41,object:[42,47,49],occupi:41,offer:41,often:[41,48],onc:[39,41,42,45,46,47],one:[39,41,45,47],ones:42,onli:[12,40,41,42,46,48],onnx:43,opac:39,open:[34,41,43,45,47,49],opt:41,optim:[41,46,48],optimis:[41,47],option:[39,41,42,45,47,49],order:[39,47],org:[2,19,20,49],orient:44,origin:[41,42,46,47,48,49],original_nam:42,os:43,other:42,otherwis:42,otsu:[41,42,48,49],our:[41,42,43,46,47,49],out:[6,40,41,42],out_channel:40,outlier:47,outlin:43,output:[40,41,42,46],outsid:49,over:[39,41,49],overal:41,overlap:42,own:[41,42,49],packag:[43,46,48,49],pad:[41,44,46],page:[29,43,46,48,49],pair:[44,48],paper:[42,46,47],paramet:[2,39,41,42,46,48],part:[2,41,46],partial:46,particularli:43,pass:[40,47],patch:[41,46],path:[41,45,46],patienc:46,paus:41,per:45,percentag:41,perfect:44,perform:[19,41,42,46,47],philipp:2,pip:[43,46,48,49],pixel:[2,41,42,46,47,48],place:40,plane:45,plateau:[46,47],platform:46,pleas:[6,14,40,41,42,43,44,46,47,48,49],plot:[41,44,45,46,48],plugin:[1,4,6,9,24,25,27,28,29,31,32,33,35,39,41,42,43,47,48],plugin_bas:[39,44,45],plugin_convert:48,plugin_crf:48,plugin_crop:39,plugin_metr:44,plugin_model_infer:42,plugin_model_train:46,plugin_review:45,plugin_review_dock:45,poor:47,popul:42,port:49,portion:39,posit:[39,42,47],possibl:46,post:[2,43],postprocess:1,potenti:[2,41,46],power:[41,44,46],pre:[41,42,46,49],precis:47,predict:[2,41,44,45,48,49],prefer:[41,46],prepar:41,present:[41,42,46],press:[39,41,44,45,46],pretrain:47,pretrained_model:40,previou:41,primari:41,probabl:[2,41],process:[2,26,41,43,46,48,49],produc:[39,41,42],program:46,progress:[40,41,42,45,47],project:[41,42,45,46,49],propag:46,properti:49,proport:[41,46],propos:20,provid:[41,42,45,46,47,49],proxim:47,pth:[40,41],purpos:[13,48],py:[1,40],pyclesperanto:49,pydens:2,pydensecrf:[2,43,48],pyqt5:49,pyside2:49,python:46,pytorch:[10,40,41,42,46,49],qt:[43,49],qualiti:[41,48],quantiti:42,quick:[41,49],quicker:46,quickli:47,quicksav:[39,41],radiu:47,rais:47,ram:42,ran:42,random:46,randomli:44,rang:[39,44,48],rate:[41,46,47],rather:42,ratio:[41,42,48],raw:46,re:[41,42,46,49],reach:[41,47],reader:[43,49],readi:[41,42,45,46],recap:45,recommend:[41,42,43,46,47,49],reconstruct:47,record:[41,46],red:44,reduc:[20,41,42,46],refer:[42,43,46,47,48],refin:[48,49],regard:49,region:[39,41,47,49],regionprop:49,registr:49,regular:[42,46],reimplement:[10,40,41,47],relat:[23,24,43,49],relev:39,reli:47,remain:39,remap:47,rememb:41,remov:[12,41,45],repeat:41,replac:[39,40],repositori:[41,43],repres:41,reproduc:[41,46],request:46,requir:[2,41,42,46,47],requisit:49,research:2,reset:39,resiz:[39,45],resolut:[39,41,42,48],restart:[39,41],result:[41,44,45,46,47,48],retain:41,retrain:[42,47],review:[33,34,39,49],rich:41,right:[39,41],robert:49,robust:47,rotat:44,roughli:41,round:48,run:[21,41,42,43,48,49],s41592:49,s:[39,41,43,45,46,48,49],sa:2,same:[39,41,42,45,46,47],sampl:[46,49],satisfactori:47,satisfi:41,save:[41,42,45,46,48],sb:2,scale:[2,39,45,47],schedul:46,score:44,scratch:41,search:43,second:39,section:[41,42,43,46,49],see:[39,41,42,43,46,48,49],seed:[41,46],seem:42,segment:[1,3,19,20,41,42,46,47,49],segresnet:[7,41,42,46],select:[39,41,42,43,45,46,48],self:40,semant:[41,42,46,49],sensit:47,separ:[41,42,46,49],seper:41,sequenti:45,session:[34,39,41,45],set:[39,42,44,46,47],setup:[0,49],sever:[23,26,42,43,46,49],sg:2,shape:2,sheet:49,shift:[41,45,46],shortcut:41,should:[41,42,44,45,46,47,49],show:[6,29,41,42],shown:[42,46],sigma:[41,47],significantli:47,similar:[41,44,47],similarli:42,simpl:48,simpli:[39,41,42,46,49],simultan:[39,41,46],singl:[41,45,46],site:46,size:[39,41,42,44,46,48],skimag:49,slice:[41,45],slider:[39,41,42],small:[41,44],smaller:[39,41,42,44,48],smooth:2,so:[41,45],soft:20,softncut:47,softwar:49,solut:43,some:41,sort:44,sourc:[43,49],spatial:[2,47],specif:[39,41,42,43],specifi:[40,41,42,46,48],speed:46,spent:41,spheric:[41,42,48],squar:47,stabil:47,stack:[42,45,46],standard:[2,47],start:[34,39,41,42,43,45,46],stat:[41,42],state:41,statist:42,statu:[41,45],step:[2,41,43,46,47],stephan:49,stick:41,still:[39,40,41],stop:[41,46],store:[41,46],strongli:49,structur:40,substanti:41,succe:42,success:[43,49],suffici:44,suggest:46,suit:41,sum:47,superior:41,supervis:[47,49],support:[6,40,41,42,43,45,46,49],sure:[41,42,45],surround:41,swin:[42,46],swinunetr:[8,41,42,46],system:[41,45,46],t:43,tab:[41,47],tabl:46,take:47,taken:[41,45],task:49,templat:6,ten:47,tensor:40,term:47,termin:43,test:[13,43],text:41,than:[41,42,48],thank:49,thei:[14,41,44,45,46,49],them:[14,41,42,43,45,46,48,49],theori:41,thi:[1,6,20,24,39,40,41,42,43,44,45,46,47,48,49],those:47,three:39,threshold:[39,41,42,44],through:46,tif:[41,42,45,46],tiff:46,time:[39,41,42,45,46,47],timokleia:49,tini:29,tissu:[41,49],todo:0,too:41,tool:[39,41,44,48,49],toolbox:49,tooltip:49,topograph:48,topographi:48,torch:[40,49],total:[41,42,48],touch:48,track:[41,42,45,46],trailmap:[9,10,15,41,42,46,49],trailmap_m:[42,46],train:[1,4,12,22,23,32,42,43,48,49],transfer:[41,46],transform:[42,46,48],truth:44,tumor:[42,46],tutori:[0,41],tverski:46,two:[41,44,46,47],under:[41,46],underneath:46,understand:[45,49],unetr:46,uniform:[41,46],uninstal:43,uniqu:[41,48],unless:41,unlik:47,unstabl:47,unsupervis:[19,20,41,47,49],unsur:41,unus:30,up:46,upcom:46,updat:[0,39,42,45],url:40,us:[1,2,6,9,12,15,22,39,41,42,43,44,45,46,47,48],usabl:41,usag:[41,46],user:[36,43,46,49],util:[23,26,28,35,39,42,43,45,46,49],valid:[41,46],valu:[41,42,46,47,48],vari:[41,44],variabl:[37,41],varianc:46,varieti:41,variou:[42,49],ve:41,veri:[41,49],verif:44,verifi:45,version:[0,9,19,20,43,46,47,49],versu:[41,46],via:[43,46,49],vidal:49,view:[41,42],viewer:[39,44,46],visibl:[39,42],visual:[45,49],visualis:41,vladlen:2,vnet:[11,41,42,46],voigt:49,volum:[33,41,42,45,46,49],volume_:41,volumetr:[42,46],voronoi:[41,42,48,49],vram:42,w1:2,w2:2,w:[2,12,19,49],wa:[20,42,47,49],wai:[0,39],wait:[46,47],wandb:43,want:[39,41,42,45],watch:47,watersh:[41,42,48],we:[40,41,43,46,49],websit:[43,46,49],weight:[2,12,14,40,41,42,43,46,47,49],weights_fil:40,well:[40,46,48,49],were:49,what:[41,49],when:[34,39,41,42,44,46,47],whenev:46,where:[41,42,45],wherea:41,whether:[42,44,45,49],which:[1,21,39,41,45,46,47],whole:[41,47,49],whose:41,widget:34,window:[41,42,43,45,48,49],wip:[40,49],wish:[41,42,49],within:[39,41,42,45,46,47],without:[41,42,43,49],wnet:[0,41,46,49],work:[39,40,41,45,46,48],worker:[1,21,22,23],worker_infer:[1,42],worker_train:[1,46],worker_util:1,workflow:[41,49],would:40,wrapper:[1,5,7,8,11,12],written:42,wrong:44,wyss:49,x:[39,40,41,42,44,45,48],xia:49,y:[39,40,41,42,44,45,48],yet:[6,41],yield:41,yml:43,you:[14,39,40,41,42,43,44,45,46,47,48,49],your:[40,41,42,43,44,45,46,47,48,49],z:[39,40,41,42,45,48],zerocostdl4m:47,zip:[41,46],zoom:39},titles:["<no title>","napari_cellseg3d.code_models","napari_cellseg3d.code_models.crf","napari_cellseg3d.code_models.instance_segmentation","napari_cellseg3d.code_models.model_framework","napari_cellseg3d.code_models.models","napari_cellseg3d.code_models.models.TEMPLATE_model","napari_cellseg3d.code_models.models.model_SegResNet","napari_cellseg3d.code_models.models.model_SwinUNetR","napari_cellseg3d.code_models.models.model_TRAILMAP","napari_cellseg3d.code_models.models.model_TRAILMAP_MS","napari_cellseg3d.code_models.models.model_VNet","napari_cellseg3d.code_models.models.model_WNet","napari_cellseg3d.code_models.models.model_test","napari_cellseg3d.code_models.models.pretrained","napari_cellseg3d.code_models.models.unet","napari_cellseg3d.code_models.models.unet.buildingblocks","napari_cellseg3d.code_models.models.unet.model","napari_cellseg3d.code_models.models.wnet","napari_cellseg3d.code_models.models.wnet.model","napari_cellseg3d.code_models.models.wnet.soft_Ncuts","napari_cellseg3d.code_models.worker_inference","napari_cellseg3d.code_models.worker_training","napari_cellseg3d.code_models.workers_utils","napari_cellseg3d.code_plugins","napari_cellseg3d.code_plugins.plugin_base","napari_cellseg3d.code_plugins.plugin_convert","napari_cellseg3d.code_plugins.plugin_crf","napari_cellseg3d.code_plugins.plugin_crop","napari_cellseg3d.code_plugins.plugin_helper","napari_cellseg3d.code_plugins.plugin_metrics","napari_cellseg3d.code_plugins.plugin_model_inference","napari_cellseg3d.code_plugins.plugin_model_training","napari_cellseg3d.code_plugins.plugin_review","napari_cellseg3d.code_plugins.plugin_review_dock","napari_cellseg3d.code_plugins.plugin_utilities","napari_cellseg3d.interface","napari_cellseg3d.utils","API reference","Cropping\u2702\ufe0f","Advanced : Custom models","Detailed walkthrough - Supervised learning","Inference\ud83d\udcca","Installation guide \u2699","Metrics utility guide \ud83d\udcc8","Review\ud83d\udd0d","Training\ud83d\udcc9","Advanced : WNet training","Utilities \ud83d\udee0","Welcome to CellSeg3D!"],titleterms:{"1":[46,48],"10":48,"2":[46,48],"3":[46,48],"3d":48,"4":48,"5":48,"6":48,"7":48,"8":48,"9":48,"function":[39,42,45],"new":39,For:46,acknowledg:49,action:48,advanc:[40,46,47],analysi:41,anisotrop:48,api:38,arm64:43,avail:48,buildingblock:16,cellseg3d:[43,49],clear:48,code:[39,42,44,45,46,48],code_model:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23],code_plugin:[24,25,26,27,28,29,30,31,32,33,34,35],common:47,condit:48,content:49,convers:41,convert:48,creat:39,crf:[2,48],crop:[39,41,48],custom:40,data:46,detail:41,detect:41,document:49,field:48,fragment:48,guid:[41,43,44],imag:[41,48],infer:[41,42],instal:[43,49],instanc:48,instance_segment:3,integr:46,interfac:[36,39,42,45],issu:47,jupyt:41,label:[41,48],larg:48,launch:[39,45],layer:39,learn:41,m1:43,m2:43,mac:43,metric:44,model:[5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,40,41,42,46],model_framework:4,model_segresnet:7,model_swinunetr:8,model_test:13,model_trailmap:9,model_trailmap_m:10,model_vnet:11,model_wnet:12,napari:49,napari_cellseg3d:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37],notebook:41,object:[41,48],option:[43,46],other:49,paramet:[44,47],plot:42,plugin:49,plugin_bas:25,plugin_convert:26,plugin_crf:27,plugin_crop:28,plugin_help:29,plugin_metr:30,plugin_model_infer:31,plugin_model_train:32,plugin_review:33,plugin_review_dock:34,plugin_util:35,pre:43,pretrain:14,process:[39,45],pyqt5:43,pyside2:43,pytorch:43,random:48,refer:[38,49],remov:48,requir:[43,44,49],requisit:43,resiz:48,result:42,review:[41,45],run:46,save:39,score:41,semant:48,set:41,small:48,soft_ncut:20,sourc:[39,42,44,45,46,48],statist:48,supervis:[41,46],tab:46,template_model:6,threshold:48,train:[41,46,47],troubleshoot:47,unet:[15,16,17],unsupervis:[42,46],up:41,us:49,usag:49,util:[37,41,44,48],volum:[39,48],walkthrough:41,wandb:46,welcom:49,wnet:[18,19,20,42,47],worker_infer:21,worker_train:22,workers_util:23,your:39}}) \ No newline at end of file diff --git a/source/guides/installation_guide.html b/source/guides/installation_guide.html index b45643cc..3e72ae35 100644 --- a/source/guides/installation_guide.html +++ b/source/guides/installation_guide.html @@ -431,6 +431,7 @@

Contents

  • Installing CellSeg3D
  • M1/M2 (ARM64) Mac installation
    • +
  • Optional requirements
    • @@ -529,6 +530,49 @@

    M1/M2 (ARM64) Mac installation +

    Optional requirements#

    +

    Several additional functionalities are available optionally. To install them, use the following commands:

    + +
    pip install pydensecrf@git+https://github.com/lucasb-eyer/pydensecrf.git#egg=master
+
    +
    + +
    pip install napari-cellseg3D[wandb]
+
    +
    + +
    pip install napari-cellseg3D[onnx-cpu]
+pip install napari-cellseg3D[onnx-gpu]
+
    +
    + +
    pip install napari-cellseg3D[docs]
+
    +
    + +
    pip install pydensecrf@git+https://github.com/lucasb-eyer/pydensecrf.git#egg=master
+pip install napari-cellseg3D[test]
+
    +
    + +
    pip install napari-cellseg3D[dev]
+
    +
    +