scPortrait
scPortrait Ecosystem
Quickstart
Installation
scPortrait workflow
Stitching
Segmentation
Extraction
Featurization
Selection
A walk through the scPortrait Ecosystem
Import Required Libraries
Generate the Project Structure
Load Imaging Data
Method 1: loading images from file
Method 2: loading images from numpy array
Looking at the loaded images
Generating a Segmentation
Looking at Segmentation Results
Extracting single-cell images
Look at extracted single-cell images
Classification of extracted single-cells
looking at the generated results
Exporting Cutting contours for excision on the LMD7
scPortrait Workflow
scPortrait Projects
Project classes
1. Project
2. TimecourseProject
Initializing a scPortrait Project
Loading Images into a scPortrait project
Config Files
spatialdata
stitching
Segmentation
Segmentation classes
1. Segmentation
2. ShardedSegmentation
3. TimecourseSegmentation
4. MultithreadedSegmentation
Segmentation Workflows
WGA segmentation
DAPI segmentation
Cytosol Cellpose segmentation
DAPI Cellpose segmentation
Extraction
Extraction classes
Single-cell image datasets
Featurization
Selection
Example Notebooks
Basic scPortrait Project
A walk through the scPortrait Ecosystem
Import Required Libraries
Generate the Project Structure
Load Imaging Data
Generating a Segmentation
Extracting single-cell images
Classification of extracted single-cells
Exporting Cutting contours for excision on the LMD7
Segmentation Workflows
Example Notebook showcasing the different segmentation workflows
WGA Segmentation
DAPI Segmentation
Cytosol Segmentation Cellpose
DAPI Segmentation Cellpose
Additional Notebooks
scPortrait tools
parsing
stitching
Example Stitching Notebook
Single-threaded Stitching
initializing the stitcher object
Generating thumbnails
Generating full-scale stitched image
Multi-threaded Stitching
initializing the stitcher object
Generating thumbnails
Generating full-scale stitched image
Visualize Stitching Output
Module API
Module Documentation
pipeline
project
Project
segmentation
Segmentation
ShardedSegmentation
segmentation workflows
extraction
HDF5CellExtraction
classification
MLClusterClassifier
CellFeaturizer
selection
LMDSelection
processing
images
masks
processing
images
masks
tools
parsing
stitching
ml
datasets
metrics
models
plmodels
pretrained_models
transforms
utils
scPortrait
Join us on GitHub
scPortrait Workflow
stitching
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stitching