spatial_proteomics
Contents:
The preprocessing (
pp
) accessor
The label (
la
) accessor
The plot (
pl
) accessor
The tool (
tl
) accessor
Tutorials:
Example Workflow with spatialproteomics
Subselecting Data
Segmentation
Custom Cropping
Plotting
Image Processing
Cell Type Prediction
Interoparability
Interactivity
spatial_proteomics
»
Welcome to the documentation of spatialproteomics!
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Welcome to the documentation of spatialproteomics!
Contents:
The preprocessing (
pp
) accessor
The label (
la
) accessor
The plot (
pl
) accessor
The tool (
tl
) accessor
Tutorials:
Example Workflow with spatialproteomics
1. Getting Started
2. Image Processing
3. Cell Segmentation
4. Quantifying Protein Expression per Cell
5. Cell Type Prediction
6. Plotting
Subselecting Data
Slicing Channels and Spatial Coordinates
Slicing Labels
Segmentation
Whole-Cell Segmentation with Cellpose
Whole-Cell Segmentation with Mesmer
Nuclear Segmentation with StarDist
Segmenting Multiple Channels with Cellpose
Custom Cropping
Loading the image from a zarr file
Drawing in the healthy regions using TissueTag
Putting the mask into the spatialproteomics object
Using the mask to set every pixel intensity to 0 in that region
Using the mask to remove cells in that region
Plotting
Plotting Channel Intensities
Rendering Segmentation Masks
Rendering Obs
Rendering Labels
Annotation of Regions or Cells
Expert Plotting
Image Processing
Cell Type Prediction
Image Processing
Cell Type Prediction with Argmax
Cell Type Prediction with Astir
Marker Binarization
Interoparability
Importing Data
Exporting Data
Exporting to Zarr
Exporting Tables to CSV
Exporting to AnnData
Exporting to SpatialData
Interactivity
Indices and tables
Index
Module Index
Search Page