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A hybrid CNN-Random Forest algorithm for bacterial spore segmentation and classification in TEM images
Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysik.
Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysik.ORCID-id: 0000-0002-0168-0197
Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysik.ORCID-id: 0000-0002-0496-6692
Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysik. Umeå universitet, Medicinska fakulteten, Umeå Centre for Microbial Research (UCMR). (The Biophysics and Biophotonics group)ORCID-id: 0000-0002-9835-3263
2023 (Engelska)Ingår i: Scientific Reports, E-ISSN 2045-2322, Vol. 13, nr 1, artikel-id 18758Artikel i tidskrift (Refereegranskat) Published
Abstract [en]

We present a new approach to segment and classify bacterial spore layers from Transmission Electron Microscopy (TEM) images using a hybrid Convolutional Neural Network (CNN) and Random Forest (RF) classifier algorithm. This approach utilizes deep learning, with the CNN extracting features from images, and the RF classifier using those features for classification. The proposed model achieved 73% accuracy, 64% precision, 46% sensitivity, and 47% F1-score with test data. Compared to other classifiers such as AdaBoost, XGBoost, and SVM, our proposed model demonstrates greater robustness and higher generalization ability for non-linear segmentation. Our model is also able to identify spores with a damaged core as verified using TEMs of chemically exposed spores. Therefore, the proposed method will be valuable for identifying and characterizing spore features in TEM images, reducing labor-intensive work as well as human bias.

Ort, förlag, år, upplaga, sidor
Springer Nature, 2023. Vol. 13, nr 1, artikel-id 18758
Nationell ämneskategori
Annan fysik Annan data- och informationsvetenskap
Identifikatorer
URN: urn:nbn:se:umu:diva-216165DOI: 10.1038/s41598-023-44212-5ISI: 001123935800008PubMedID: 37907463Scopus ID: 2-s2.0-85175591485OAI: oai:DiVA.org:umu-216165DiVA, id: diva2:1809565
Forskningsfinansiär
Vetenskapsrådet, 2019-04016Kempestiftelserna, JCK-2129.3Tillgänglig från: 2023-11-04 Skapad: 2023-11-04 Senast uppdaterad: 2025-09-30Bibliografiskt granskad
Ingår i avhandling
1. Spotlight the killer: detecting harmful chemical and biological agents using optical spectroscopy
Öppna denna publikation i ny flik eller fönster >>Spotlight the killer: detecting harmful chemical and biological agents using optical spectroscopy
2025 (Engelska)Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
Alternativ titel[sv]
Lyset på mördaren : detektion av skadliga kemiska och biologiska ämnen med hjälp av optisk spektroskopi
Abstract [en]

Harmful chemical and biological agents are a significant threat to health and prosperity worldwide. Recent years have seen an increase in wars and conflicts around the globe, raising concerns about the potential deployment of chemical and biological warfare agents. On a less speculative level, harmful chemicals such as narcotic substances cause immense humanitarian and economic damage through overdoses and associated healthcare costs, while microbes such as pathogenic bacteria and parasites cause hospital-acquired infections and food spoilage at a cost of approximately 1 trillion euros every year. To combat the threat of these harmful agents, we must thus develop rapid and effective detection and diagnostic methods for harmful agents, allowing us to effectively deploy specific treatments and preventative measures.

Classically, while there exist numerous methods for the detection of both harmful chemical and biological agents, they often come with limitations that inhibit their effectiveness. These inhibitions often take the form of bulky equipment that is difficult to apply in the field or time-consuming preparation and measurement processes.

In this thesis we will explore an alternative category of assays for detecting and characterizing harmful materials – optical spectroscopy. Optical spectroscopy is a category of material characterization methods that use light to probe a material. While probing the material, we receive a signal characteristic of the molecules, chemical, and biological structure of our material. These optical spectroscopic methods, such as Raman spectroscopy and fluorescence spectroscopy, can be used to characterize a material within the span of minutes or even seconds, making them ideal for detection applications. Furthermore, they can often be made portable or even handheld, making them a great tool for initial field indication of harmful materials, ahead of thorough lab analysis.

I sincerely hope the studies presented herein can serve as a stepping stone to future technologies and detection assays, capable of saving both money and lives. 

Ort, förlag, år, upplaga, sidor
Umeå: Umeå University, 2025. s. 72
Nyckelord
Sensing, Raman spectroscopy, SERS, Fluorescence spectroscopy, CWA, nerve agents, bacterial spores, Cryptosporidium
Nationell ämneskategori
Atom- och molekylfysik och optik
Identifikatorer
urn:nbn:se:umu:diva-244830 (URN)978-91-8070-780-0 (ISBN)978-91-8070-779-4 (ISBN)
Disputation
2025-10-24, Aula Anatomica, Biologihuset, 907 36, Umeå, Umeå, 13:00 (Engelska)
Opponent
Handledare
Anmärkning

This work was done in collaboration with, and with support from, the Swedish Defece Research Agency (FOI).

Tillgänglig från: 2025-10-03 Skapad: 2025-09-30 Senast uppdaterad: 2025-10-22Bibliografiskt granskad

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Qamar, SaqibÖberg, RasmusMalyshev, DmitryAndersson, Magnus

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Qamar, SaqibÖberg, RasmusMalyshev, DmitryAndersson, Magnus
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