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Installation
Tutorials
Welcome to the world of Whole slide images!
Preprocessing a WSI: From raw image to analysis-ready data
WSI Visualization in LazySlide
Cell segmentation tutorial
Feature extraction and spatial analysis
Integration with slide-level labels
Integration with transcriptomics
Zero-shot learning
Survival prediction with cancer WSIs
Approximate segmentation through tile prediction
Virtual Staining: Zero-Cost Multiplexed Imaging from H&E Images
Histology tile generation
Model Zoo
API Reference
Preprocessing:
pp
lazyslide.pp.find_tissues
lazyslide.pp.tile_tissues
lazyslide.pp.tile_graph
Tools:
tl
lazyslide.tl.feature_extraction
lazyslide.tl.feature_aggregation
lazyslide.tl.spatial_features
lazyslide.tl.tissue_props
lazyslide.tl.tile_prediction
lazyslide.tl.spatial_domain
lazyslide.tl.tile_shaper
lazyslide.tl.text_embedding
lazyslide.tl.text_image_similarity
lazyslide.tl.RNALinker
lazyslide.tl.zero_shot_score
lazyslide.tl.slide_caption
lazyslide.tl.virtual_stain
lazyslide.tl.image_generation
Plotting:
pl
lazyslide.pl.tissue
lazyslide.pl.tiles
lazyslide.pl.annotations
lazyslide.pl.WSIViewer
Segmentation
seg
lazyslide.seg.cells
lazyslide.seg.cell_types
lazyslide.seg.semantic
lazyslide.seg.tissue
lazyslide.seg.artifact
IO
io
lazyslide.io.load_annotations
lazyslide.io.export_annotations
Models
lazyslide_models.list_models
lazyslide_models.vision.CHIEF
lazyslide_models.vision.CTransPath
lazyslide_models.vision.GPFM
lazyslide_models.vision.GenBioPathFM
lazyslide_models.vision.GigaPath
lazyslide_models.vision.H0Mini
lazyslide_models.vision.HOptimus0
lazyslide_models.vision.HOptimus1
lazyslide_models.vision.HibouB
lazyslide_models.vision.HibouL
lazyslide_models.vision.LunitDINOPatch8
lazyslide_models.vision.LunitDINOPatch16
lazyslide_models.vision.LunitResNet50BT
lazyslide_models.vision.LunitResNet50MoCoV2
lazyslide_models.vision.LunitResNet50SwAV
lazyslide_models.vision.Midnight
lazyslide_models.vision.OpenMidnight
lazyslide_models.vision.PathOrchestra
lazyslide_models.vision.Phikon
lazyslide_models.vision.PhikonV2
lazyslide_models.vision.UNI
lazyslide_models.vision.UNI2
lazyslide_models.vision.Virchow
lazyslide_models.vision.Virchow2
lazyslide_models.multimodal.BiomedCLIP
lazyslide_models.multimodal.CONCH
lazyslide_models.multimodal.MUSK
lazyslide_models.multimodal.MedSigLip
lazyslide_models.multimodal.OmiCLIP
lazyslide_models.multimodal.PLIP
lazyslide_models.multimodal.Prism
lazyslide_models.multimodal.QuiltNetB16
lazyslide_models.multimodal.QuiltNetB16PMB
lazyslide_models.multimodal.QuiltNetB32
lazyslide_models.multimodal.Titan
lazyslide_models.segmentation.Cellpose
lazyslide_models.segmentation.GrandQCArtifact
lazyslide_models.segmentation.GrandQCTissue
lazyslide_models.segmentation.HESTTissueSegmentation
lazyslide_models.segmentation.HistoPLUS
lazyslide_models.segmentation.Instanseg
lazyslide_models.segmentation.NuLite
lazyslide_models.segmentation.PathProfilerTissueSegmentation
lazyslide_models.segmentation.SAM
lazyslide_models.segmentation.SMPBase
lazyslide_models.tile_prediction.FocusLiteNN
lazyslide_models.tile_prediction.PathProfilerQC
lazyslide_models.tile_prediction.SpiderBreast
lazyslide_models.tile_prediction.SpiderColorectal
lazyslide_models.tile_prediction.SpiderSkin
lazyslide_models.tile_prediction.SpiderThorax
lazyslide_models.multimodal.Prism
lazyslide_models.multimodal.Titan
lazyslide_models.vision.CHIEFSlideEncoder
lazyslide_models.vision.GigaPathSlideEncoder
lazyslide_models.vision.MadeleineSlideEncoder
lazyslide_models.vision.Moozy
lazyslide_models.tile_prediction.cv_features.Brightness
lazyslide_models.tile_prediction.cv_features.Canny
lazyslide_models.tile_prediction.cv_features.Contrast
lazyslide_models.tile_prediction.cv_features.Entropy
lazyslide_models.tile_prediction.cv_features.HaralickTexture
lazyslide_models.tile_prediction.cv_features.Saturation
lazyslide_models.tile_prediction.cv_features.Sharpness
lazyslide_models.tile_prediction.cv_features.Sobel
lazyslide_models.tile_prediction.cv_features.SplitRGB
lazyslide_models.style_transfer.GigaTIME
lazyslide_models.style_transfer.ROSIE
lazyslide_models.image_generation.CytoSyn
lazyslide_models.base.ImageGenerationModel
lazyslide_models.base.ImageModel
lazyslide_models.base.ImageTextModel
lazyslide_models.base.ModelBase
lazyslide_models.base.SegmentationModel
lazyslide_models.base.SlideEncoderModel
lazyslide_models.base.StyleTransferModel
lazyslide_models.base.TilePredictionModel
lazyslide_models.base.TimmModel
Computer vision utilities
lazyslide.cv.Mask
lazyslide.cv.BinaryMask
lazyslide.cv.MultilabelMask
lazyslide.cv.MulticlassMask
lazyslide.cv.InstanceMap
lazyslide.cv.ProbabilityMap
lazyslide.cv.merge_connected_polygons
lazyslide.cv.nms
Metrics
lazyslide.metrics.segmentation.SegmentationStats
lazyslide.metrics.segmentation.get_instance_stats
lazyslide.metrics.segmentation.get_semantic_stats
lazyslide.metrics.segmentation.accuracy
lazyslide.metrics.segmentation.precision
lazyslide.metrics.segmentation.recall
lazyslide.metrics.segmentation.f1_score
lazyslide.metrics.segmentation.mean_iou
lazyslide.metrics.segmentation.dice
lazyslide.metrics.segmentation.sensitivity
lazyslide.metrics.segmentation.specificity
lazyslide.metrics.segmentation.pq
lazyslide.metrics.topk
Contributing
Setup development environment
Submission of new models
Release cycle of LazySlide
Contributors
Glossary
References
.rst
.pdf
lazyslide.cv.BinaryMask
Contents
BinaryMask
lazyslide.cv.BinaryMask
#
class
BinaryMask
(
mask
,
prob_map
=
None
,
class_names
=
None
)
#
Bases:
Mask
Contents
BinaryMask
