New software enables automated analysis of biomedical image data without programming knowledge

New software enables automated analysis of biomedical image data without programming knowledge

by Ronja Münch, Leibniz Institute for Organic Solution Research and An infection Biology – Hans Knoell Institute –

JIPipe can be utilised, for instance, to assess the movement profiles of nematodes. Credit score: Hannah Büttner, Zoltán Cseresnyés, Ruman Gerst / Leibniz-HKI

The software package JIPipe was developed by scientists at the Leibniz Institute for All-natural Product Investigation and Infection Biology (Leibniz-HKI) and substantially simplifies the investigation of visuals generated in research. Buyers can produce flowcharts according to their application requires and therefore carry out automatic picture analyses working with artificial intelligence without any programming know-how. JIPipe is centered on ImageJ, a typical program for scientific investigation of biomedical microscopic visuals. The authors now existing their improvement in Character Strategies.

Illustrations or photos, particularly microscopic pictures, play a significant function in biomedical investigation. With the help of fluorescent labels, for instance, processes in cells turn into seen. “A picture is value a thousand words—that is however accurate,” claims Thilo Figge, head of the Utilized Units Biology investigate group at Leibniz-HKI and professor at Friedrich Schiller University Jena.

But assessment poses escalating difficulties for researchers. “Increased and better resolutions and consequently larger sized quantities of facts are becoming produced,” Figge explains. “At the identical time, the procedures of AI, or artificial intelligence, are now so innovative that they are ever more tough to use for researchers without having programming competencies.”

The open up resource plan JIPipe—short for Java Graphic Processing Pipeline—developed at Leibniz-HKI aims to simplify that. “JIPipe is a device that does not require any programming skills,” points out developer Ruman Gerst, a member of the Used Methods Biology investigation team. Alternatively, the program employs a visual programming language: with the support of prefabricated constructing blocks, end users can make particular person workflows to instantly examine pictures in accordance to their distinct prerequisites.

Scientific image analysis for everyone
Screenshot of a JIPipe assessment of nematode survival. Credit history: Zoltán Cseresnyés/Leibniz-HKI

JIPipe supports other programming languages

The program is centered on the open resource software ImageJ, which has proven alone as a regular in scientific impression evaluation. JIPipe and ImageJ are fully suitable and enhance each individual other in scientific graphic evaluation. “Our software supports ImageJ scripts and involves the standard features and macros,” Gerst explains. Other programming languages these kinds of as Python and R are also supported.

The precursor method was developed quite a few several years back by Zoltán Cseresnyés, also a member of the Utilized Techniques Biology investigation group. “At first, I wrote the code for a phagocytosis assay,” Cseresnyés explains. In phagocytosis, a cell requires up a particle, these kinds of as a different cell, and breaks it down, which is usually visualized with fluorescent dyes.

Above time, the imaging expert kept extending the code for new programs, and the plan grew to become unwieldy and much too advanced. “We recognized we had to redesign it and make it modular,” Cseresnyés says, which is why the staff brought bioinformatician Ruman Gerst on board. He also advised the recent visible programming language, which makes it possible for the staff to review picture info from any biomedical difficulty.

Reproducible results

JIPipe has currently been utilised for several studies, for case in point to look into the performance of drug shipping and delivery by so-identified as nanocarriers in the liver or to take a look at the survival level of nematodes that have digested toxin-developing microorganisms. Confrontations in between immune cells and fungal spores have also been analyzed with the new plan. The builders also present programs for use as section of the Microverse Imaging Centre and the NFDI4BioImage, component of the German Nationwide Investigation Information Infrastructure.

“In contrast to manual image analysis, automatic assessment often offers the similar success, is as a result reproducible and complies with the so-referred to as Fair ideas for image analysis,” Thilo Figge emphasizes. The expression Truthful originates in the area of study facts administration and stands for “Findable, Accessible, Interoperable and Reusable.”

A lot more info:
Ruman Gerst et al, JIPipe: visual batch processing for ImageJ, Nature Strategies (2023). DOI: 10.1038/s41592-022-01744-4


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