Microlist – Microscopy courses, software, meetings & jobs

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A searchable database of resources
for light microscopists

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Our latest submissions

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Principal Scientist, Imaging

For Novartis
In Cambridge

Senior Scientist, Imaging

For Novartis
In Cambridge

Research Scientist, Imaging

For Novartis
In Cambridge

Some of our favs

Featured Listings

Microcourses YouTube Channel

Short videos on microscopy fundamentals

Microforum

The light microscopy discussion forum

Image Analysis Forum: image.sc

The image analysis discussion forum

Browse

Categories

Courses

Software & Other Tools

eLearning

Conferences & Symposia

Tools for microscopists

Getting things done

Micro-Manager2 MacroExtensions

Allows ImageJ to access Micro-Manager2 functionalities
Created by Jerome Mutterer

Image and Data Analysis Core Software List

A list of open-source software for image analysis

Multi-view simulation

Code for simulating a multiview acquisition
Created by Preibisch Lab

Ray Optics Simulation

Simulate reflection and refraction of light
Created by Rick Tu

Multi-view reconstruction

Software for reconstruction of multiview images
Created by Preibisch Lab

Napari

Fast ND image viewer for python
Created by Sofroniew, Royer, Nunez-Iglesias et al (doi:10.5281/zenodo.3555620)

Chroma Spectraviewer

A spectraviewer from the company Chroma
Created by Chroma Technology Corporation

BigStitcher

Stitching for large datasets
Created by Preibisch Lab

LLSpy-SLM

Python app for generating SLM masks for lattice light sheet
Created by Talley Lambert, Harvard Medical School

BisQue

Store, visualize, organize and analyze in the cloud
Created by UCSB Center for Bio-image Informatics

miCube Open Source Microscope

Plans to build your own fluorescence microscope
Created by Hohlbein Lab

Thermo Fisher Scientific Fluorescence Spectraviewer

Fluorescence spectraviewer
Created by Thermo Fisher Scientific Inc

OpenFlexure Microscope

an open-source 3D-printed microscope
Created by R Bowman et al

QuPath

software for whole slide image analysis
Created by Pete Bankhead and Jose Fernandez

smfBox

Build a single molecule FRET box
Created by Craggs Lab

Pixel Chart

Learn how an image histogram is formed
Created by Andrei Kashcha

CIDRE

A flatfield illumination correction method
Created by Horvath Lab

Icy

Platform for bioimage informatics
Created by Quantitative Image Analysis Unit, Institut Pasteur

Mesmerize: A highly versatile platform for calcium imaging analysis

Platform for Calcium imaging analysis
Created by Kushal Kolar, Daniel Dondorp, Marios Chatzigeorgiou

ilastik

Interactive learning and segmentation toolkit
Created by Anna Kreshuk's lab, EMBL

Browse by Technique

What are you in to?

Fluorescent Proteins

8 listings

Super-Resolution Microscopy

7 listings

58 listings

Light Sheet Microscopy

14 listings

Quantitative Microscopy

5 listings

Machine Learning

17 listings

Confocal Microscopy

10 listings

7 listings

Fluorescence Microscopy

15 listings

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Microscopy Courses

Nothing beats full immersion

Master's Degree Programme in Biomedical Imaging

Location: Turku, Finland

Master of Science in Microscopy and Imaging

Location: Galway, Ireland

Nikon Imaging Center at Harvard Medical School Workshops

Format: In-person
Location: Boston, MA

Widening the Lens - Fall 2022

Format: Remote / Virtual

Resources by Location

Where do you want to be?

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