sebgoti

ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse

BatchConvert

A nextflow based tool that wraps bfconvert and bioformats2raw to convert image data collections to OME-TIFF and OME-Zarr, respectively, in a parallelised manner.

baysor-nextflow-module

Nextflow module to use Baysor for cell segmentation in imaging-based Spatial Transcriptomics

micro-sam

Segment Anything for Microscopy

napari-spacetx-explorer

A simple plugin for an interactive visualization of spatial omics data.

Jupyter-Napari-Desktop

Example tutorial for setting up a jupyter desktop remote proxy with napari.

thesis_page

Baysor

Bayesian Segmentation of Spatial Transcriptomics Data

pystackreg

A python extension for the automatic alignment of a source image or a stack (movie) to a target image/reference frame.

stimwrap

advanced_machine_learning

Code to go along the lecture course "Advanced Machine Learning for Physics, Science, and Artificial Scientific Discovery"

stracking

python library for particles tracking in 2D+t and 3D+t scientific images

starfish

starfish: unified pipelines for image-based transcriptomics

napari-spot-detection-tutorial

A tutorial on performing spot detection using napari, scikit-image, and scipy

ngff

Next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.

napari

napari: a fast, interactive, multi-dimensional image viewer for python

scikit-image

Image processing in Python

Cell-Motility-System-for-the-CPM

Ongoing work on cell motility system for the CPM using Morpheus, FitMultiCell, and Python

FitMultiCell_Tutorial

Contains code and morpheus files used as a FitMultiCell tutorial for parameter estimation and model selection.

MachineLearningA-Z

General working directory for Machine Learning projects.