FPBioimage

Description

FPBioimage is a volumetric visualization tool which runs in all modern web browsers. Try the tool yourself at our example site here.

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PYME

Description

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

CellProfiler Analyst CPA

Description

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.

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Image Data Explorer

Description

The Image Data Explorer is a Shiny app that allows the interactive visualization of images and ROIs associated with data points shown in a scatter plot. It is useful for exploring the relationships between images/ROIs and associated data represented in tabular format.

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EvaluateSegmentation Tool

Description

A command line tool that allows to quantitatively compare two volumes of binary segmentations. Implements 22 different metrics for comparing segmentations such as Dice Coefficient, Hausdorff Distance and average Distance. 

Snakemake

Description

A Python based workflow management software that allows to create workflows that seamlessly scale from a single workstation to a high performance computing cluster or cloud environments. 

Automated workflow for parallel Multiview Reconstruction

Description

Automated workflow for performing multiview reconstruction of large multiview, multichannel, multiillumination time-lapse SPIM data on a high performance computing (HPC) cluster or on a single workstation. 

YeastSpotter

Description

Code to segment yeast cells using a pre-trained mask-rcnn model. We've tested this with yeast cells imaged in fluorescent images and brightfield images, and gotten good results with both modalities. This code implements an user-friendly script that hides all of the messy implementation details and parameters. Simply put all of your images to be segmented into the same directory, and then plug and go.

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MSRC Registration Toolbox

Description

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 Microscopy10.1021/acs.analchem.8b02884

  • Next Generation Histology-directed Imaging Mass Spectrometry Driven by Autofluorescence Microscopy10.1021/acs.analchem.8b02885

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Nuclei Segmentation (ilastik)

Description

NEUBIAS-WG5 workflow for nuclei segmentation using ilastik v1.3.2 and Python post-processing.

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