Pinned Repositories
3i-utils
My 3i SlideBook utilities
bioimagebook.github.io
An introduction to bioimage analysis - http://bioimagebook.github.io
Imaris
My Imaris plugins
libapt
An Open Source rewrite of the Thorlabs APT.dll based on the cross-platform libftdi1 library
libatrous
My "A trous" wavelet library with Python bindings.
micromanager-upstream
Micro-Manager Open Source Microscopy Software (http://valelab.ucsf.edu/~MM/MMwiki/). SVN-tracking Git repository
uPyLoader
File transfer and communication tool for MicroPython boards
ypipe
Hardware device (STM32duino based) for spying on RS232 communications
zindy's Repositories
zindy/Imaris
My Imaris plugins
zindy/ypipe
Hardware device (STM32duino based) for spying on RS232 communications
zindy/bioimagebook.github.io
An introduction to bioimage analysis - http://bioimagebook.github.io
zindy/BoZoN
Minimalist Drag & drop file sharing app (version 2.4 build 15)
zindy/cellpose
a generalist algorithm for cellular segmentation
zindy/cellprofiler_plugins
My CellProfiler plugins
zindy/czitools_lite
This repository provides a collection of tools to simplify reading CZI (Carl Zeiss Image) pixel and metadata in Python. In addition it also contains other useful utilities to visualize CZI images inside Napari.
zindy/dams
An IDE (editor, assembler, debugger) for Amstrad CPC
zindy/GUI_AutoTH_QuPath
zindy/md2googleslides
Generate Google Slides from markdown
zindy/NanoJ-Fluidics
Manual, source-code and binaries for the NanoJ-Fluidics project
zindy/napari
napari: a fast, interactive, multi-dimensional image viewer for python
zindy/napari-czifile2
Carl Zeiss Image (.czi) file support for napari
zindy/piccolo
A fast, user friendly ORM and query builder which supports asyncio.
zindy/piccolo_admin
A powerful web admin for your database.
zindy/piccolo_api
ASGI middleware for authentication, rate limiting, and building CRUD endpoints.
zindy/pytrackmate
Import Trackmate XML files in Python as Pandas dataframe
zindy/qupath
QuPath - Open Source Digital Pathology
zindy/QuPath-Auto-Threshold
QuPath script to apply various auto-threshold methods from ImageJ on annotations.
zindy/qupath-docs
QuPath documentation
zindy/qupath-extension-align
QuPath extension to interactively align images
zindy/qupath-extension-cellpose
an extension that wraps a Cellpose environment such that WSI can be analyzed using Cellpose through QuPath.
zindy/qupath-extension-jinput
jinput support for QuPath navigation (3Dconnexion SpaceMouse)
zindy/qupath-fxtras
Reusable JavaFX tools for QuPath (and beyond)
zindy/qupath-translations
QuPath Translation effort
zindy/RICS
RICS notes
zindy/SlicerSandbox
Collection of utilities that are not polished implementations but can be useful to users
zindy/Spellcheck-Website-Tampermonkey-Script
Enables browser and plugin spell checking ability within static website content. Simplifies QA workflows when no other tools or text source access are viable alternatives.
zindy/transferwee
Download/upload files via wetransfer.com
zindy/valis
Virtual Alignment of pathoLogy Image Series