This repository contains NiftyRegSGD: A GPU based high peformance non-rigid image registration

Acquire: a multi-camera video streaming software focusing on microscopy

navigate - open source light-sheet microscope controls

A cross-platform GUI automation Python module for human beings. Used to programmatically control the mouse & keyboard.

Execution engine for microscope control

Tools for distributed alignment of massive images

independent stage map widget

Python Library for using PI controllers with GCS command language

Mecademic Python API

Processing of raw ratiometric biosensor images (for example based on FRET) into fully corrected "ratio maps" or "activation maps" — images showing the localized activation of the biosensor.

a lightweight python interface for ASI brand Tiger Controllers

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

A pre-commit hook for Ruff.

Correcting lens-distortion in confocal stacks

Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Python

Schema.org Data Models for HTAN

Old academic project for my PhD - no longer maintained by me: fast gaussian and derivative convolutional filters

Scope2Screen is an open-source web-application for focus+context exploration and annotation of whole-slide, high-plex, tissue images.

Composable transformations of Python+NumPy programs: differentiate, vectorize, JIT to GPU/TPU, and more

TensorFlow Deconvolution for Microscopy Data

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

B³D compression library

Source code for molecular graphics program UCSF ChimeraX

Smart rotation analysis code