Semi-automated

The PYthon Microscopy Environment is an open-source package providing image acquisition and data analysis functionality for a number of microscopy applications, but with a particular emphasis on single molecule localisation microscopy (PALM/STORM/PAINT etc ...). The package is multi platform, running on Windows, Linux, and OSX.

It comes with 3 main modules:

• PYMEAcquire - Instrument control and simulation
• dh5view - Image Data Analysis and Viewing
• VisGUI - Visualising Localization Data Sets

Fiji plugin for detecting, tracking and quantifying filopodia

CellProfiler Analyst (CPA) allows interactive exploration and analysis of data, particularly from high-throughput, image-based experiments. Included is a supervised machine learning system which can be trained to recognize complicated and subtle phenotypes, for automatic scoring of millions of cells. CPA provides tools for exploring and analyzing multidimensional data, particularly data from high-throughput, image-based experiments analyzed by its companion image analysis software, CellProfiler.

This python toolbox performs registration between 2-D microscopy images from the same tissue section or serial sections in several ways to achieve imaging mass spectrometry (IMS) experimental goals.

This code supports the following works and enables others to perform the workflows outlined in the following works, please cite them if you use this toolbox:

• Advanced Registration and Analysis of MALDI Imaging Mass Spectrometry Measurements through Autofluorescence Microscopy, 10.1021/acs.analchem.8b02884

• Next Generation Histology-directed Imaging Mass Spectrometry Driven by Autofluorescence Microscopy, 10.1021/acs.analchem.8b02885

ImageJ/FIJI plugin generating contour lines with equal spacing on top of an image (using overlay).