Three-dimensional (3D) segmentation of cells in microscopy images is crucial to accurately capture signals that extend across optical sections. Using brightfield images for segmentation has the advantage of being minimally phototoxic and leaving all other channels available for signals of interest. However, brightfield images only readily provide information for two-dimensional (2D) segmentation. In radially symmetric cells, such as fission yeast and many bacteria, this 2D segmentation can be computationally extruded into the third dimension. However, current methods typically make the simplifying assumption that cells are straight rods. Here, we report Pomegranate, a pipeline that performs the extrusion into 3D using spheres placed along the topological skeletons of the 2D-segmented regions. The diameter of these spheres adapts to the cell diameter at each position. Thus, Pomegranate accurately represents radially symmetric cells in 3D even if cell diameter varies and regardless of whether a cell is straight, bent or curved. We have tested Pomegranate on fission yeast and demonstrate its ability to 3D segment wild-type cells as well as classical size and shape mutants. The pipeline is available as a macro for the open-source image analysis software Fiji/ImageJ. 2D segmentations created within or outside Pomegranate can serve as input, thus making this a valuable extension to the image analysis portfolio already available for fission yeast and other radially symmetric cell types.
- Award ID(s):
- 1941808
- NSF-PAR ID:
- 10403485
- Date Published:
- Journal Name:
- ACM Transactions on Graphics
- Volume:
- 41
- Issue:
- 6
- ISSN:
- 0730-0301
- Page Range / eLocation ID:
- 1 to 11
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
more » « less
Abstract -
more » « less
Abstract We present a method that detects boundaries of parts in 3D shapes represented as point clouds. Our method is based on a graph convolutional network architecture that outputs a probability for a point to lie in an area that separates two or more parts in a 3D shape. Our boundary detector is quite generic: it can be trained to localize boundaries of semantic parts or geometric primitives commonly used in 3D modeling. Our experiments demonstrate that our method can extract more accurate boundaries that are closer to ground‐truth ones compared to alternatives. We also demonstrate an application of our network to fine‐grained semantic shape segmentation, where we also show improvements in terms of part labeling performance.
-
There are many realistic applications of activity recognition where the set of potential activity descriptions is combinatorially large. This makes end-to-end supervised training of a recognition system impractical as no training set is practically able to encompass the entire label set. In this paper, we present an approach to fine-grained recognition that models activities as compositions of dynamic action signatures. This compositional approach allows us to reframe fine-grained recognition as zero-shot activity recognition, where a detector is composed “on the fly” from simple first-principles state machines supported by deep-learned components. We evaluate our method on the Olympic Sports and UCF101 datasets, where our model establishes a new state of the art under multiple experimental paradigms. We also extend this method to form a unique framework for zero-shot joint segmentation and classification of activities in video and demonstrate the first results in zero-shot decoding of complex action sequences on a widely-used surgical dataset. Lastly, we show that we can use off-the-shelf object detectors to recognize activities in completely de-novo settings with no additional training.more » « less
-
Memory latency and bandwidth are significant bottlenecks in designing in-memory indexes. Processing-in-memory (PIM), an emerging hardware design approach, alleviates this problem by embedding processors in memory modules, enabling low-latency memory access whose aggregated bandwidth scales linearly with the number of PIM modules. Despite recent work in balanced comparison-based indexes on PIM systems, building efficient tries for PIMs remains an open challenge due to tries' inherently unbalanced shape. This paper presents the PIM-trie, the first batch-parallel radix-based index for PIM systems that provides load balance and low communication under adversary-controlled workloads. We introduce trie matching-matching a query trie of a batch against the compressed data trie-as a key building block for PIM-friendly index operations. Our algorithm combines (i) hash-based comparisons for coarse-grained work distribution/elimination and (ii) bit-by-bit comparisons for fine-grained matching. Combined with other techniques (meta-block decomposition, selective recursive replication, differentiated verification), PIM-trie supports LongestCommonPrefix, Insert, and Delete in O(logP) communication rounds per batch and O(l/w) communication volume per string, where P is the number of PIM modules, l is the string length in bits, and w is the machine word size. Moreover, work and communication are load-balanced among modules whp, even under worst-case skew.more » « less
-
more » « less
Abstract Large‐scale digitization projects such as
#ScanAllFishes andoVert are generating high‐resolution microCT scans of vertebrates by the thousands. Data from these projects are shared with the community using aggregate 3D specimen repositories like MorphoSource through various open licenses. We anticipate an explosion of quantitative research in organismal biology with the convergence of available data and the methodologies to analyse them.Though the data are available, the road from a series of images to analysis is fraught with challenges for most biologists. It involves tedious tasks of data format conversions, preserving spatial scale of the data accurately, 3D visualization and segmentations, and acquiring measurements and annotations. When scientists use commercial software with proprietary formats, a roadblock for data exchange, collaboration and reproducibility is erected that hurts the efforts of the scientific community to broaden participation in research.
We developed SlicerMorph as an extension of 3D Slicer, a biomedical visualization and analysis ecosystem with extensive visualization and segmentation capabilities built on proven python‐scriptable open‐source libraries such as Visualization Toolkit and Insight Toolkit. In addition to the core functionalities of Slicer, SlicerMorph provides users with modules to conveniently retrieve open‐access 3D models or import users own 3D volumes, to annotate 3D curve and patch‐based landmarks, generate landmark templates, conduct geometric morphometric analyses of 3D organismal form using both landmark‐driven and landmark‐free approaches, and create 3D animations from their results. We highlight how these individual modules can be tied together to establish complete workflow(s) from image sequence to morphospace. Our software development efforts were supplemented with short courses and workshops that cover the fundamentals of 3D imaging and morphometric analyses as it applies to study of organismal form and shape in evolutionary biology.
Our goal is to establish a community of organismal biologists centred around Slicer and SlicerMorph to facilitate easy exchange of data and results and collaborations using 3D specimens. Our proposition to our colleagues is that using a common open platform supported by a large user and developer community ensures the longevity and sustainability of the tools beyond the initial development effort.
- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1145/3550454.3555440
