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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
Model Zoo
API Reference
Preprocessing:
pp
lazyslide.pp.find_tissues
lazyslide.pp.score_tissues
lazyslide.pp.tile_tissues
lazyslide.pp.score_tiles
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
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.CONCHVision
lazyslide.models.vision.CTransPath
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.Midnight
lazyslide.models.vision.PLIPVision
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.CONCH
lazyslide.models.multimodal.MUSK
lazyslide.models.multimodal.OmiCLIP
lazyslide.models.multimodal.PLIP
lazyslide.models.multimodal.Prism
lazyslide.models.multimodal.Titan
lazyslide.models.segmentation.Cellpose
lazyslide.models.segmentation.GrandQCArtifact
lazyslide.models.segmentation.GrandQCTissue
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.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.ROSIE
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.scorer.FocusLite
lazyslide.cv.scorer.Contrast
lazyslide.cv.scorer.SplitRGB
lazyslide.cv.scorer.Redness
lazyslide.cv.scorer.Brightness
lazyslide.cv.scorer.ScorerBase
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
References
.rst
.pdf
lazyslide.models.base.SlideEncoderModel
Contents
SlideEncoderModel
lazyslide.models.base.SlideEncoderModel
#
class
SlideEncoderModel
#
Bases:
ModelBase
Contents
SlideEncoderModel
