journal article·2024-10Open access

Quality control of immunofluorescence images using artificial intelligence

Madhavi Dipak Andhari, Giulia Rinaldi, Pouya Nazari, Johanna Vets, Gautam Shankar, Nikolina Dubroja, Tessa Ostyn, Maxime Vanmechelen, Brecht Decraene, Alexandre Arnould, Willem Mestdagh, Bart De Moor, Frederik De Smet, Francesca Bosisio, Asier Antoranz

Cell Reports Physical Science· Volume 5· Issue 10

Abstract

sponsorship: M.D.A. is supported by KU Leuven grant EHU-D6472-C 16/19/006. M.V. is supported by FWO PhD fellowship fundamental research (11L0824N) . A. Antoranz is supported by a postdoctoral fellowship senior grant from FWO (12ATN24N) . F.B. is supported by FWO Fundamenteel Klinisch Mandaat EMH-D8972-FKM/20. B.D.M. is funded by the KU Leuven Research Fund (projects iBOF/23/064, C16/15/059, C3/19/053, C24/18/022, C3/20/117, and C3I-21-00316) ; the KU Leuven Industrial Research Fund: EOS project no. G0F6718N (SeLMA) , SBO project S005319N, infrastructure project I013218N, and TBM project T001919N; a PhD grant (SB/1SA1319N) ; EWI: the Flanders AI Research Program, VLAIO: CSBO (HBC.2021.0076) Baekeland PhD (HBC.20192204) ; the European Commission: European Research Council under the European Union's Horizon 2020 research and innovation program; and the Foundation "Kom op tegen Kanker,"CM (Christelijke Mutualiteit) . (KU Leuven grant|EHU-D6472-C 16/19/006, FWO PhD fellowship fundamental research|11L0824N, FWO|12ATN24N, FWO Fundamenteel Klinisch Mandaat|EMH-D8972-FKM/20, KU Leuven Research Fund|iBOF/23/064, KU Leuven Research Fund|C16/15/059, KU Leuven Research Fund|C3/19/053, KU Leuven Research Fund|C24/18/022, KU Leuven Research Fund|C3/20/117, KU Leuven Research Fund|C3I-21-00316, KU Leuven Industrial Research Fund: EOS project|G0F6718N, KU Leuven Industrial Research Fund: EOS project|S005319N, KU Leuven Industrial Research Fund: EOS project|I013218N, TBM project|T001919N, PhD grant|SB/1SA1319N, EWI: the Flanders AI Research Program, VLAIO: CSBO|HBC.2021.0076, EWI: the Flanders AI Research Program, VLAIO: CSBO|HBC.20192204, European Commission: European Research Council, Foundation "Kom op tegen Kanker,"CM (Christelijke Mutualiteit))
Source: openalex_inverted_index · Quality: baseline

Research context

OpenAlex topics: Image Processing Techniques and Applications · AI in cancer detection · Cell Image Analysis Techniques

SciVX discovery tags are terminology-based. OpenAlex topics are source-provided classifications.

References (50)

Show source-provided references
1. 2023
2. Next-Generation Pathology Using Multiplexed Immunohistochemistry: Mapping Tissue Architecture at Single-Cell Level10.3389/fonc.2022.918900 ↗
3. Mapping the Immune Landscape in Metastatic Melanoma Reveals Localized Cell–Cell Interactions That Predict Immunotherapy Response10.1158/0008-5472.CAN-22-0363 ↗
4. MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging10.1038/s41592-021-01308-y ↗
5. A framework for multiplex imaging optimization and reproducible analysis10.1038/s42003-022-03368-y ↗
6. Multiplex Immunofluorescence Image Quality Checking Using DAPI Channel-referenced Evaluation10.1369/00221554231161693 ↗
7. Quality Control for High-Throughput Imaging Experiments Using Machine Learning in Cellprofiler
8. Workflow and metrics for image quality control in large-scale high-content screens10.1177/1087057111420292 ↗
9. A review of artifacts in histopathology10.4103/jomfp.JOMFP_125_15 ↗
10. The Effect of Quality Control on Accuracy of Digital Pathology Image Analysis10.1109/JBHI.2020.3046094 ↗
11. Deep Learning for Whole Slide Image Analysis: An Overview10.3389/fmed.2019.00264 ↗
12. Blur image detection using Laplacian operator and Open-CV
13. Eliminating tissue-fold artifacts in histopathological whole-slide images for improved image-based prediction of cancer grade10.4103/2153-3539.117448 ↗
14. Deep learning in histopathology: the path to the clinic10.1038/s41591-021-01343-4 ↗
15. Complexity of ballooned hepatocyte feature recognition: Defining a training atlas for artificial intelligence-based imaging in NAFLD10.1016/j.jhep.2022.01.011 ↗
16. HistoQC: An Open-Source Quality Control Tool for Digital Pathology Slides10.1200/CCI.18.00157 ↗
17. Artifact Detection and Restoration in Histology Images with Stain-Style and Structural Preservation10.1109/TMI.2023.3288940 ↗
18. Abstract 5442: SlideQC: An AI-based tool for automated quality control of whole-slide digital pathology images10.1158/1538-7445.AM2023-5442 ↗
19. Focus Quality Assessment of High-Throughput Whole Slide Imaging in Digital Pathology10.1109/TMI.2019.2919722 ↗
20. QC-Automator: Deep Learning-Based Automated Quality Control for Diffusion MR Images
21. ArtSeg—Artifact segmentation and removal in brightfield cell microscopy images without manual pixel-level annotations10.1038/s41598-022-14703-y ↗
22. ImageNet: A large-scale hierarchical image database
23. Transfer learning for medical image classification: a literature review10.1186/s12880-022-00793-7 ↗
24. Automated classification of histopathology images using transfer learning10.1016/j.artmed.2019.101743 ↗
25. Deep convolutional neural network VGG-16 model for differential diagnosing of papillary thyroid carcinomas in cytological images: a pilot study10.7150/jca.28769 ↗
26. Chollet · 2015
27. Iakubovskii · 2023
28. Fully automated sequential immunofluorescence (seqIF) for hyperplex spatial proteomics10.1038/s41598-023-43435-w ↗
29. CODEX multiplexed tissue imaging with DNA-conjugated antibodies10.1038/s41596-021-00556-8 ↗
30. Visualizing Data using t-SNE
31. An Analysis of Active Learning Strategies for Sequence Labeling Tasks
32. A Survey of Deep Active Learning
33. Entropy-based active learning for object recognition
34. Localized Motion Artifact Reduction on Brain MRI Using Deep Learning with Effective Data Augmentation Techniques
35. Artifact Detection in Lung Ultrasound: An Analytical Approach10.3390/electronics12071551 ↗
36. Automatic Artifact Removal from Dermoscopic Images
37. In-depth characterization of the tumor microenvironment in central nervous system lymphoma reveals implications for immune-checkpoint therapy10.1007/s00262-020-02575-y ↗
38. Tradeoffs Using Binary and Multiclass Neural Network Classification for Medical Multidisease Detection
39. Multiple Iterative Labeling by Antibody Neodeposition (MILAN).
40. Single-cell spatial proteomics depicts novel dynamics involving senescent progenitors in fibrotic lesions in COPD and IPF
41. Transcriptional and spatial profiling of the kidney allograft unravels a central role for FcyRIII+ innate immune cells in rejection10.1038/s41467-023-39859-7 ↗
42. Multiomics and spatial mapping characterizes human CD8+ T cell states in cancer10.1126/scitranslmed.add1016 ↗
43. A TCF4-dependent gene regulatory network confers resistance to immunotherapy in melanoma10.1016/j.cell.2023.11.037 ↗
44. NIH Image to ImageJ: 25 years of image analysis10.1038/nmeth.2089 ↗
45. How transferable are features in deep neural networks?
46. Adam: A Method for Stochastic Optimization
47. On evaluation metrics for medical applications of artificial intelligence10.1038/s41598-022-09954-8 ↗
48. Receiver Operating Characteristic (ROC) Curve Analysis for Medical Diagnostic Test Evaluation
49. A Survey on Performance Metrics for Object-Detection Algorithms
50. 2024