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Microscopy analysis neural network to solve detection, enumeration and segmentation from image-level annotations

Nature Machine Intelligence volume 4, pages 455–466 (2022)Cite this article

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A preprint version of the article is available at bioRxiv.

Abstract

The development of deep learning approaches to detect, segment or classify structures of interest has transformed the field of quantitative microscopy. High-throughput quantitative image analysis presents a challenge due to the complexity of the image content and the difficulty to retrieve precisely annotated datasets. Methods capable of reducing the annotation burden associated with the training of a deep neural network on microscopy images becomes primordial. Here we introduce a weakly supervised MICRoscopy Analysis neural network (MICRA-Net) that can be trained on a simple main classification task using image-level annotations to solve multiple more complex tasks such as semantic segmentation. MICRA-Net relies on the latent information embedded within a trained model to achieve performances similar to established architectures when no precisely annotated dataset is available. This learnt information is extracted from the network using gradient class activation maps, which are combined to generate detailed feature maps of the biological structures of interest. We demonstrate how MICRA-Net substantially alleviates the expert annotation process on various microscopy datasets and can be used for high-throughput quantitative analysis of microscopy images.

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Fig. 1: Various supervision levels can be employed for training a DL model to segment structures of interest in microscopy images.
Fig. 2: MICRA-Net architecture and experimental results on the modified MNIST dataset.
Fig. 3: Semantic segmentation of F-actin nanostructures observed on super-resolution microscopy images.
Fig. 4: Semantic instance segmentation on five selected cell lines of the CTC dataset.
Fig. 5: Detection of Giemsa-stained red blood cells from two different datasets of brightfield microscopy images from ref. 38.
Fig. 6: MICRA-Net is used as a tool to assist experts in the detection of sparse axon DAB markers in large SEM images of ultrathin mouse brain sections.

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Data availability

The MNIST, Cell Tracking Challenge and P. vivax datasets are all publicly available online. The F-actin and EM dataset are available at https://s3.valeria.science/flclab-micranet/index.html.

Code availability

Open source code for the MICRA-Net approach is available at https://github.com/FLClab/MICRA-Net and https://doi.org/10.5281/zenodo.5949132.

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Acknowledgements

We acknowledge the following: L. Emond for F-actin sample preparation and immunocytochemistry; F. Nault, C. Salesse and L. Emond for the neuronal cell culture; J. Marek and R. Bernatchez for the development of a custom Python annotation application; T. Dhellemmes for inter-expert axon DAB annotations in EM images; C. Gagné and M.-A. Gardner for preliminary discussions on semantic segmentation; A. Schwerdtfeger and A. Gabela for careful proofreading of the manuscript. Funding was provided by grants from the Natural Sciences and Engineering Research Council of Canada (RGPIN-2017-06171, P.D.K.; RGPIN-2018-06264, M.P.; RGPIN-2019-06704, F.L.-C.), Canadian Institutes of Health Research (153107, P.D.K.; 470155, M.P.), Neuronex Initiative (Fond de Recherche du Québec—Santé; 295823, P.D.K. and F.L.-C.), CERVO Brain Research Center Foundation (F.L.-C.) and the Canadian Foundation for Innovation (32786, P.D.K.; 39088, F.L.-C.). F.L.-C. is a Canada Research Chair Tier II (CRC-2019-00126, F.L.-C.), A.D. is a CIFAR AI Chair, and A.B. is supported by a PhD scholarship from the Fonds de Recherche du Québec—Nature et Technologie (FRQNT) and an excellence scholarship from the FRQNT strategic cluster UNIQUE.

Author information

Authors and Affiliations

  1. CERVO Brain Research Center, Québec, Québec, Canada

    Anthony Bilodeau, Constantin V. L. Delmas, Martin Parent, Paul De Koninck, Audrey Durand & Flavie Lavoie-Cardinal

  2. Institute for Intelligence and Data, Québec, Québec, Canada

    Anthony Bilodeau, Audrey Durand & Flavie Lavoie-Cardinal

  3. Department of Psychiatry and Neuroscience, Université Laval, Québec, Québec, Canada

    Martin Parent & Flavie Lavoie-Cardinal

  4. Department of Biochemistry, Microbiology, and Bioinformatics, Université Laval, Québec, Québec, Canada

    Paul De Koninck

  5. Department of Computer Science and Software Engineering, Université Laval, Québec, Québec, Canada

    Audrey Durand

  6. Department of Electrical and Computer Engineering, Université Laval, Québec, Québec, Canada

    Audrey Durand

  7. Canada CIFAR AI Chair, Québec, Québec, Canada

    Audrey Durand

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Contributions

A.B. and F.L.-C. designed the approach. A.B. implemented the neuronal network architectures, generated the modified MNIST dataset, created the annotation application for the user study and performed all deep learning experiments. A.B., A.D. and F.L.-C. analysed the results. F.L.-C. acquired and annotated the F-actin dataset. C.V.L.D. and M.P. generated and provided the annotated EM dataset. F.L.-C., A.D. and P.D.K. supervised the project. F.L.-C., A.D. and A.B. wrote the manuscript.

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Correspondence to Flavie Lavoie-Cardinal.

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Nature Machine Intelligence thanks Alexander Krull and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Extended data

Extended Data Fig. 1 Graphical user interface (GUI) developed to facilitate the visualisation of the extracted local maps from MICRA-Net.

Graphical user interface (GUI) developed to facilitate the visualisation of the extracted local maps from MICRA-Net. The detailed instructions to use the application can be found on the GitHub repository (https://github.com/FLClab/MICRA-Net). Briefly, one can load a trained MICRA-Net model and an image to predict the presence of a specific structure. The GUI shows the extracted local maps L1−8 to the user for each activated class of the selected image. The user can select the desired local maps which are combined into a detailed feature map that can be thresholded to generate a final segmentation mask.

Extended Data Fig. 2 Representative images of F-actin semantic segmentation on dendrites for both structures.

Representative images of F-actin semantic segmentation on dendrites for both structures (fibers and periodical lattice [rings]). From left to right, the fine segmentation from the Expert, MICRA-Net, weakly supervised U-Net, weakly supervised Mask R-CNN and Ilastik are shown. The color code maps true positive (TP, green), false positive (FP, yellow) and false negative (FN, red) segmentation for each method compared to the fine Expert labels. A red arrow indicates a region in the periodical lattice image missed by the Expert. Scale bars 1μm.

Extended Data Fig. 3 Representative examples of the instance segmentation procedure using MICRA-Net for two cell lines of the Cell Tracking Challenge.

Representative examples of the instance segmentation procedure using MICRA-Net for two cell lines of the Cell Tracking Challenge (top: PhC-C2DL-PSC, bottom: Fluo-N2DL-HeLa). Shown are the input image (left), the PCA decomposition of the raw feature maps extracted from layers L1−7 of MICRA-Net for the cell prediction (middle, and the grad-CAM of layer L8 for semantic contact (right). Scale bars: 25 μm.

Extended Data Fig. 4 Schematic of the training and fine-tuning procedure for MICRA-Net on the P. Vivax dataset.

Schematic of the training and fine-tuning procedure for MICRA-Net on the P. Vivax dataset. a) Data preparation: 80/20 split of the provided training set is used for training and validation respectively, keeping the testing set as is. b) Fine-tuning of MICRA-Net: uniform sample of {12, 24, 36} images from the testing set. A 3-fold scheme is used: training on two folds and validating on a separate fold, enabling early stopping. The 3-fold allowed to calculate the total number of epochs to train each model and to set the detection thresholds. All methods were tested on the same testing set of 84 images. c) Training: 5 different models were trained on the original dataset (Naive). For fine-tuning, the 3-fold scheme was repeated 5 times, one time for each of the 5 Naive models as starting points, generating a total of 25 models. Thus, allowing to stop the fine-tuning at a specific epoch.

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Bilodeau, A., Delmas, C.V.L., Parent, M. et al. Microscopy analysis neural network to solve detection, enumeration and segmentation from image-level annotations. Nat Mach Intell 4, 455–466 (2022). https://doi.org/10.1038/s42256-022-00472-w

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