BANKSY: spatial clustering

Local Spatial Gradient Inference

Code for the TAURUS study

Integrative Spatial Analysis of H&E and IHC Images Identifies Prognostic Immune Subtypes correlated with Progression Free Survival in HPV-Related Oropharyngeal Squamous Cell Carcinoma

tools and notes for spatial omics

https://www.sc-best-practices.org

A novel machine learning pipeline to analyse spatial transcriptomics data

Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoCycler / MACSima / etc.)

Blazing fast nuclei segmentation for brightfield Whole Slide Images

Code used to benchmark Xenium

Non-disruptive collagen characterization in clinical histopathology using cross-modality image synthesis

One Model is All You Need: Multi-Task Learning Enables Simultaneous Histology Image Segmentation and Classification

❄️🔥 Visual Prompt Tuning [ECCV 2022] https://arxiv.org/abs/2203.12119

A curated list of prompt-based paper in computer vision and vision-language learning.

Tools for dividing pathology whole slide images into tiles and save them as individual files.

Use this to download all elements of the BCSS dataset described in: Amgad M, Elfandy H, ..., Gutman DA, Cooper LAD. Structured crowdsourcing enables convolutional segmentation of histology images. …

Open source tools for computational pathology - Nature BME

tutorials for wsi analysis by Hongming Xu

Differentiable ODE solvers with full GPU support and O(1)-memory backpropagation.

Jupyter notebook with Pytorch implementation of Neural Ordinary Differential Equations

tensorboard for pytorch (and chainer, mxnet, numpy, ...)

Code for "Latent ODEs for Irregularly-Sampled Time Series" paper

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