Automated Segmentation and Morphometry of Cell and Tissue Structures. Selected Algorithms in ImageJ

Prodanov, Dimiter; Verstreken, Kris

doi:10.5772/36729

Cited by 24 publications

(13 citation statements)

References 31 publications

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“…Gaussian or median filter functions in ImageJ or Imaris) or by convolving the image with a mathematical morphology operation (i.e. opening or closing) [129].…”

Section: Image Segmentationmentioning

confidence: 99%

Probing the 3D architecture of the plant nucleus with microscopy approaches: challenges and solutions

Dumur

Duncan

Graumann

et al. 2019

Nucleus

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The eukaryotic cell nucleus is a central organelle whose architecture determines genome function at multiple levels. Deciphering nuclear organizing principles influencing cellular responses and identity is a timely challenge. Despite many similarities between plant and animal nuclei, plant nuclei present intriguing specificities. Complementary to molecular and biochemical approaches, 3D microscopy is indispensable for resolving nuclear architecture. However, novel solutions are required for capturing cell-specific, sub-nuclear and dynamic processes. We provide a pointer for utilising high-to-super-resolution microscopy and image processing to probe plant nuclear architecture in 3D at the best possible spatial and temporal resolution and at quantitative and cell-specific levels. High-end imaging and image-processing solutions allow the community now to transcend conventional practices and benefit from continuously improving approaches. These promise to deliver a comprehensive, 3D view of plant nuclear architecture and to capture spatial dynamics of the nuclear compartment in relation to cellular states and responses. Abbreviations: 3D and 4D: Three and Four dimensional; AI: Artificial Intelligence; ant: antipodal nuclei (ant); CLSM: Confocal Laser Scanning Microscopy; CTs: Chromosome Territories; DL: Deep Learning; DLIm: Dynamic Live Imaging; ecn: egg nucleus; FACS: Fluorescence-Activated Cell Sorting; FISH: Fluorescent In Situ Hybridization; FP: Fluorescent Proteins (GFP, RFP, CFP, YFP, mCherry); FRAP: Fluorescence Recovery After Photobleaching; GPU: Graphics Processing Unit; KEEs: KNOT Engaged Elements; INTACT: Isolation of Nuclei TAgged in specific Cell Types; LADs: Lamin-Associated Domains; ML: Machine Learning; NA: Numerical Aperture; NADs: Nucleolar Associated Domains; PALM: Photo-Activated Localization Microscopy; Pixel: Picture element; pn: polar nuclei; PSF: Point Spread Function; RHF: Relative Heterochromatin Fraction; SIM: Structured Illumination Microscopy; SLIm: Static Live Imaging; SMC: Spore Mother Cell; SNR: Signal to Noise Ratio; SRM: Super-Resolution Microscopy; STED: STimulated Emission Depletion; STORM: STochastic Optical Reconstruction Microscopy; syn: synergid nuclei; TADs: Topologically Associating Domains; Voxel: Volumetric pixel

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“…Gaussian or median filter functions in ImageJ or Imaris) or by convolving the image with a mathematical morphology operation (i.e. opening or closing) [129].…”

Section: Image Segmentationmentioning

confidence: 99%

Probing the 3D architecture of the plant nucleus with microscopy approaches: challenges and solutions

Dumur

Duncan

Graumann

et al. 2019

Nucleus

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“…After whole-mounted on glass slides, eggs were viewed under light microscopy with objective lens magnification set to x10, and photographed on a Wild Heerbrugg M400 ZOOM Makroskop (Leica, Germany) coupled to Nikon digital sight DS - Fi1 digital camera. All measurements were produced with ImageJ version 1.51 [34] and drawings were done by image overlay in Adobe Photoshop CS2 version 9.0.1.…”

Section: Methodsmentioning

confidence: 99%

Morphological and genomic characterisation of the hybrid schistosome infecting humans in Europe reveals a complex admixture between Schistosoma haematobium and Schistosoma bovis parasites

Kincaid-Smith

Tracey

Augusto

et al. 2018

Preprint

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Schistosomes cause schistosomiasis, the world’s second most important parasitic disease after malaria. A peculiar feature of schistosomes is their ability to produce viable and fertile hybrids. Originally only present in the tropics, schistosomiasis is now also endemic in Europe. Based on two genetic markers the European species had been identified as a hybrid between the ruminant-infective Schistosoma bovis and the human-infective Schistosoma haematobium.Here we describe for the first time the genomic composition of the European schistosome hybrid (77% of S. haematobium and 23% of S. bovis origins), its morphometric parameters and its compatibility with the European vector snail and intermediate host Compatibility is a key parameter for the parasites life cycle progression. We also show that egg morphology (a classical diagnostic parameter) does not allow for differential diagnosis while genetic tests do so. Additionally, we performed genome assembly improvement and annotation of S. bovis, the parental species for which no satisfactory genome assembly was available.For the first time since the discovery of hybrid schistosomes, these results reveal at the whole genomic level a complex admixture of parental genomes highlighting (i) the high permeability of schistosomes to other species’ alleles, and (ii) the importance of hybrid formation for pushing species boundaries not only conceptionally but also geographically.

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“… Example of a chronic neuroinflammatory response to implantation of a silicon probe . (A) GFAP staining after 6 weeks of implantation in tethered configuration; (B) NeuN from the same section (C) The full NeuN image was thresholded and the area fraction is plotted as a function of distance (Prodanov and Verstreken, 2012 ) to the insertion track (D) . The neuronal cell gap is clearly visible.…”

Section: Timetable Of the Implantation Effectsmentioning

confidence: 99%

Mechanical and Biological Interactions of Implants with the Brain and Their Impact on Implant Design

2016

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Neural prostheses have already a long history and yet the cochlear implant remains the only success story about a longterm sensory function restoration. On the other hand, neural implants for deep brain stimulation are gaining acceptance for variety of disorders including Parkinsons disease and obsessive-compulsive disorder. It is anticipated that the progress in the field has been hampered by a combination of technological and biological factors, such as the limited understanding of the longterm behavior of implants, unreliability of devices, biocompatibility of the implants among others. While the field's understanding of the cell biology of interactions at the biotic-abiotic interface has improved, relatively little attention has been paid on the mechanical factors (stress, strain), and hence on the geometry that can modulate it. This focused review summarizes the recent progress in the understanding of the mechanisms of mechanical interaction between the implants and the brain. The review gives an overview of the factors by which the implants interact acutely and chronically with the tissue: blood-brain barrier (BBB) breach, vascular damage, micromotions, diffusion etc. We propose some design constraints to be considered in future studies. Aspects of the chronic cell-implant interaction will be discussed in view of the chronic local inflammation and the ways of modulating it.

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Automated Segmentation and Morphometry of Cell and Tissue Structures. Selected Algorithms in ImageJ

Cited by 24 publications

References 31 publications

Probing the 3D architecture of the plant nucleus with microscopy approaches: challenges and solutions

Probing the 3D architecture of the plant nucleus with microscopy approaches: challenges and solutions

Morphological and genomic characterisation of the hybrid schistosome infecting humans in Europe reveals a complex admixture between Schistosoma haematobium and Schistosoma bovis parasites

Mechanical and Biological Interactions of Implants with the Brain and Their Impact on Implant Design

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