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timtreis / 2023_Arevalo_BatchCorrection
Forked from carpenter-singh-lab/2023_Arevalo_NatComm_BatchCorrectionEvaluating batch correction methods for image-based cell profiling
Snakemake pipeline used to segment the cpg0016 dataset of the JUMP-Cell Painting Consortium
Rapids_singlecell: A GPU-accelerated tool for scRNA analysis. Offers seamless scverse compatibility for efficient single-cell data processing and analysis.
Image-based profiling and machine learning to predict failing vs. non-failing cardiac fibroblasts
Single cell Morphology Quality Control (coSMicQC)
Image analysis and image-based profiling of a fibrosis drug screen to identify compound hits using a machine learning model.
Turn an existing conda environment into a Singularity container
OpenResume is a powerful open-source resume builder and resume parser. https://open-resume.com/
Compendium of tools for the Imaging Platform
Single Cell Extraction and Morphological Analysis of Whole Slide Images
repo for ISBI 2024 "LightMyCells" challenge
First place algorithm in ISBI 2024 Light My Cell competition, label-free cell painting
Remap, mask, renumber, unique, and in-place transposition of 3D labeled images. Point cloud too.
Python and R SOMA APIs using TileDB’s cloud-native format. Ideal for single-cell data at any scale.
Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey and dual-gene plot in high-resolution SVG/PNG format. It also…
A tool for exploration of multiomic phenotypic space
Nextflow pipeline for Targeted-Learning of genetic effects
A pure Julia implementation of the Targeted Minimum Loss-based Estimation
Scripts associated with the 2023 Open Problems competition
Different agents and different keys for different projects, with ssh.
Segment Anything for Microscopy
Segmentation method able to detect membrane/nuclei-labelled cells with low signal-to-noise ratio and dense packing in 2D and 3D. Available via pip package vollseg.