Open-source Microscopy
Open-source Microscopy - Related Videos
07:38
Open-source Single-particle Analysis for Super-resolution Microscopy with VirusMapper
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Cited by 9 •
2017
This manuscript uses the Fiji-based open-source software package VirusMapper to apply single-particle analysis to super-resolution microscopy images in order to generate precise models of nanoscale structure.
11:30
Quantitative Analysis of Aspergillus nidulans Growth Rate using Live Microscopy and Open-Source Software
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Cited by 1 •
2021
We present a label-free live imaging protocol using transmitted light microscopy techniques to capture images, analyze and quantify growth kinetics of the filamentous fungus A. nidulans in both submerged cultures and solid media. This protocol can be used in conjunction with fluorescence microscopy.
09:30
Open Source High Content Analysis Utilizing Automated Fluorescence Lifetime Imaging Microscopy
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Cited by 14 •
2017
We present an open source high content analysis (HCA) instrument utilizing automated fluorescence lifetime imaging (FLIM) for assaying protein interactions using Förster resonance energy transfer (FRET) based readouts. Data acquisition for this openFLIM-HCA instrument is controlled by software written in µManager and data analysis is undertaken in FLIMfit.
10:13
Working with Hot and Cold Sources
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2023
Source: Robert M. Rioux & Suprita Jharimune, Pennsylvania State University, University Park, PA Working with extreme temperatures, both high and low, is an integral part of many laboratory operations. For many, mentioning a laboratory instantly evokes the mental picture of a Bunsen burner. Bunsen burners and hot plates are used extensively in small and large operations in research laboratories and industries, thus making it necessary for all users to be aware of their safe handling...
01:30
Misinformation & Source Credibility
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2026
The rapid expansion of online information has increased access to knowledge while also increasing the risk of misinformation. Sources that appear authoritative may lack scholarly rigor, which makes credibility assessment a critical part of research literacy. Evaluating the reliability of information helps prevent the inclusion of weak, biased, or misleading material in academic work. Publication Source and Authorship A primary consideration is the publication source. Scholarly journals and...
FAQs
Modular design allows engineers to alter illumination, sample positioning, imaging, and analysis components without redesigning the entire instrument. This flexibility helps match the microscope to a specific experimental requirement and supports rapid prototyping. It also makes it easier to incorporate improvements or adaptations developed by different laboratories, rather than limiting the system to a fixed commercial configuration.
Open access lets users inspect how the instrument and its software operate, identify opportunities for modification, and share improved versions. This transparency supports reproducible measurement because laboratories can examine and communicate the design choices behind their systems. Compared with proprietary platforms, openly documented tools also reduce dependence on a single manufacturer when researchers need specialized capabilities.
These elements address different stages of measurement. Illumination supplies the conditions needed to examine a sample, positioning places the relevant region for observation, and digital acquisition records the image. Software then supports image analysis and interpretation. Treating these stages as adaptable components allows engineers to configure the workflow around the sample and the information the experiment must obtain.
A typical adaptation begins by identifying the experimental need, then selecting or modifying available optical, positioning, acquisition, and software components. Users can construct a customized instrument from accessible plans, adjust the configuration, and share resulting modifications with other laboratories. This workflow connects instrument design with measurement requirements and supports iterative development rather than requiring a complete system from one source.
It is particularly useful when researchers need low-cost instrument development, rapid prototyping, or a measurement system tailored to a specific task. Engineering groups can apply it to materials characterization and device fabrication while retaining the ability to modify the instrument and analysis software. Shared designs can also help laboratories build on one another's work instead of repeating development independently.
Open-source microscopy can support reproducible measurement and customized digital imaging in several areas. In engineering, it contributes to examining materials and studying fabricated devices; in other research contexts, the same adaptable approach can support biological imaging. The combination of modifiable hardware, digital acquisition, and accessible analysis helps align the instrument with the evidence each investigation requires.