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Measuring the organization of the cellular cytoskeleton and the surrounding extracellular matrix (ECM) is currently of wide interest as changes in both local and global alignment can highlight alterations in cellular functions and material properties of the extracellular environment. Different approaches have been developed to quantify these structures, typically based on fiber segmentation or on matrix representation and transformation of the image, each with its own advantages and disadvantages. Here we present AFT − Alignment by Fourier Transform , a workflow to quantify the alignment of fibrillar features in microscopy images exploiting 2D Fast Fourier Transforms (FFT). Using pre-existing datasets of cell and ECM images, we demonstrate our approach and compare and contrast this workflow with two other well-known ImageJ algorithms to quantify image feature alignment. These comparisons reveal that AFT has a number of advantages due to its grid-based FFT approach. 1) Flexibility in defining the window and neighborhood sizes allows for performing a parameter search to determine an optimal length scale to carry out alignment metrics. This approach can thus easily accommodate different image resolutions and biological systems. 2) The length scale of decay in alignment can be extracted by comparing neighborhood sizes, revealing the overall distance that features remain anisotropic. 3) The approach is ambivalent to the signal source, thus making it applicable for a wide range of imaging modalities and is dependent on fewer input parameters than segmentation methods. 4) Finally, compared to segmentation methods, this algorithm is computationally inexpensive, as high-resolution images can be evaluated in less than a second on a standard desktop computer. This makes it feasible to screen numerous experimental perturbations or examine large images over long length scales. Implementation is made available in both MATLAB and Python for wider accessibility, with example datasets for single images and batch processing. Additionally, we include an approach to automatically search parameters for optimum window and neighborhood sizes, as well as to measure the decay in alignment over progressively increasing length scales.
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Iterative Paraphrastic Augmentation with Discriminative Span Alignment
Abstract We introduce a novel paraphrastic augmentation strategy based on sentence-level lexically constrained paraphrasing and discriminative span alignment. Our approach allows for the large-scale expansion of existing datasets or the rapid creation of new datasets using a small, manually produced seed corpus. We demonstrate our approach with experiments on the Berkeley FrameNet Project, a large-scale language understanding effort spanning more than two decades of human labor. With four days of training data collection for a span alignment model and one day of parallel compute, we automatically generate and release to the community 495,300 unique (Frame,Trigger) pairs in diverse sentential contexts, a roughly 50-fold expansion atop FrameNet v1.7. The resulting dataset is intrinsically and extrinsically evaluated in detail, showing positive results on a downstream task.
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- Award ID(s):
- 1749025
- PAR ID:
- 10293091
- Date Published:
- Journal Name:
- Transactions of the Association for Computational Linguistics
- Volume:
- 9
- ISSN:
- 2307-387X
- Page Range / eLocation ID:
- 494 to 509
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1162/tacl_a_00380
