flexscspace 1.1.0

The update to SCSpace provides more flexible version options

FlexScspace

Multi-Version Enhanced scRNA-seq Spatial Reconstruction Toolkit

Flexible Versioned Spatial Analysis Toolkit
Extending scSpace with multiple algorithm implementations for optimal single-cell spatial reconstruction

Quick Navigation

• Features
• Installation
• [Quick Start](#-quick start)
• [Version Guide](#-version comparison)

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Features

• Six Algorithm Versions: v0 through v3c
• Unified API: Switch versions with one parameter

Installation

pip install FlexScspace  # Requires Python≥3.8, pytorch, scanpy

Quick Start

Common Usage(v0/v1/v2/v3b/v3c)

# Initialize with selected version
from FlexScspace import VersionSelector
algorithm = VersionSelector(version="v2")
# Load data (consistent across versions)
sc_obj, st_obj = algorithm.load_data(
    sc_data_path="sc_data.csv",
    st_data_path="st_data.csv",
    spatial_key=['imagerow','imagecol']
)
# Process data
sc_obj, st_obj = algorithm.preprocess(
    sc_adata=sc_obj,
    st_adata=st_obj,
    n_features=2000)
# Spatial reconstruction
sc_obj, st_obj = algorithm.construct_pseudo_space(
    sc_adata=sc_obj,
    st_adata=st_obj,
    batch_size=16,
    epoch_num=1000
)

v3a Specific Usage

# Initialize with selected version
from FlexScspace import VersionSelector
algorithm = VersionSelector(version="v3a")
# Load data (consistent across versions)
sc_obj, st_obj = algorithm.load_data(
    sc_data_path="sc_data.csv",
    st_data_path="st_data.csv",
    spatial_key=['imagerow','imagecol']
)
# Process data
sc_obj, st_obj = algorithm.preprocess(
    sc_adata=sc_obj,
    st_adata=st_obj,
    n_features=2000,
    r_binary=r_path,
    output_dir=output_dir)
# Spatial reconstruction
sc_obj, st_obj = algorithm.construct_pseudo_space(
    sc_adata=sc_obj,
    st_adata=t_obj,
    batch_size=16,
    epoch_num=1000
)

Version Comparison

Versions	Key Innovation	Recommended Use Case
v0	Basic version	Baseline comparisons
v1	Spatially variable gene	Tissues with clear spatial gradients
v2	Implicit Neural Representation	To be explored
v3.a	Batch correction:CCA	To be explored
v3.b	Batch correction:Scanorama	To be explored
v3.c	Batch correction:scVi	Tissues with complex organization