TomoEED: fast edge-enhancing denoising of tomographic volumes

Moreno, Juan José Hurtado; Martínez-Sánchez, Antonio; Martínez, José A.; Garzón, Eduardo Garzón; Fernández, José‐Jesús

doi:10.1093/bioinformatics/bty435

Cited by 18 publications

(16 citation statements)

References 9 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This zone corresponds to the area previously displayed in the inset of Fig. 1 C. A) Oriented 20 nm-thick slice of a filtered reconstruction ( Moreno et al, 2018 ) in which densities are visible on both sides of the cellular and flagellar membranes. Cytoplasmic sticks of the FAZ filament (white arrows) are longer and more regularly arranged than the flagellar densities facing them (white arrowheads).…”

Section: Resultsmentioning

confidence: 76%

“…S2 ). After denoising of the data using an edge-enhancing noise-reduction anisotropic diffusion filter ( Moreno et al, 2018 ), some short densities in the flagellar compartment are observed facing the cytoplasmic sticks ( Fig. 3 A, arrowheads).…”

Section: Resultsmentioning

confidence: 99%

“…Fiducial-based alignment and weighted back-projection reconstruction of the tilt-series were performed in Etomo (v.4.9.10) ( Kremer et al, 1996 , Mastronarde and Held, 2017 ). After reconstruction, 3D volumes were processed using an edge-enhancing noise-reduction anisotropic diffusion filter to enhance ultrastructural details typically using 10 to 20 iterations ( Moreno et al, 2018 ). Exploration of the reconstructed volumes and segmentations were performed in semi-automatic mode using ImageJ ( Schneider et al, 2012 ).…”

Section: Methodsmentioning

confidence: 99%

See 2 more Smart Citations

In situ structural analysis of the flagellum attachment zone in Trypanosoma brucei using cryo-scanning transmission electron tomography

Trépout

2020

Journal of Structural Biology: X

View full text Add to dashboard Cite

Highlights Flagellar and cellular membranes are in close contact next to the FAZ filament. Sticks are heterogeneously distributed along the FAZ filament length. Thin appendages are present between the sticks and the neighbouring microtubules. The FAZ could elongate thanks to the action of dynein on subpellicular microtubules.

show abstract

Section: Resultsmentioning

confidence: 76%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

In situ structural analysis of the flagellum attachment zone in Trypanosoma brucei using cryo-scanning transmission electron tomography

Trépout

2020

Journal of Structural Biology: X

View full text Add to dashboard Cite

show abstract

“…The tomograms were binned 4 times to improve contrast prior to segmentation, thus the voxel size of the final segmentations was 1.684 nm (HeLa cell and mouse neuron) and 1.368 nm (yeast). The contrast of one tomogram of yeast (EMD-10767) was enhanced prior to segmentation using an anisotropic filter [ 58 ], while the contrast of the other tomogram of yeast (EMD-10765) and the one of the mouse neuron was enhanced using a deconvolution filter executed in MATLAB (MathWorks) using the functionalities of the TOM toolbox [ 59 ]. Membrane segmentations were generated automatically from tomograms using TomoSegMemTV [ 18 ] using parameters = 10 and = 0.3 (HeLa cell), = 12 and = 4 (yeast) and = 10 and = 3 (mouse neuron) and further refined manually using Amira Software ( ThermoFisher Scientific ).…”

Section: Methodsmentioning

confidence: 99%

Reliable estimation of membrane curvature for cryo-electron tomography

et al. 2020

View full text Add to dashboard Cite

Curvature is a fundamental morphological descriptor of cellular membranes. Cryo-electron tomography (cryo-ET) is particularly well-suited to visualize and analyze membrane morphology in a close-to-native state and molecular resolution. However, current curvature estimation methods cannot be applied directly to membrane segmentations in cryo-ET, as these methods cannot cope with some of the artifacts introduced during image acquisition and membrane segmentation, such as quantization noise and open borders. Here, we developed and implemented a Python package for membrane curvature estimation from tomogram segmentations, which we named PyCurv. From a membrane segmentation, a signed surface (triangle mesh) is first extracted. The triangle mesh is then represented by a graph, which facilitates finding neighboring triangles and the calculation of geodesic distances necessary for local curvature estimation. PyCurv estimates curvature based on tensor voting. Beside curvatures, this algorithm also provides robust estimations of surface normals and principal directions. We tested PyCurv and three well-established methods on benchmark surfaces and biological data. This revealed the superior performance of PyCurv not only for cryo-ET, but also for data generated by other techniques such as light microscopy and magnetic resonance imaging. Altogether, PyCurv is a versatile open-source software to reliably estimate curvature of membranes and other surfaces in a wide variety of applications.

show abstract

“…XTEND data series were processed as described previously (28) using python scripts. Tomographic reconstructions were performed using TOMO3D software, 30 iterations of simultaneous iterative reconstruction technique (SIRT) algorithm (29) and edge enhanced using TOMOEED (30). Segmentation of volumes was carried out with SuRVoS (31), and volumes were represented with Chimera (32) and ImageJ (33).…”

Section: Methodsmentioning

confidence: 99%

Four-Dimensional Characterization of the Babesia divergens Asexual Life Cycle, from the Trophozoite to the Multiparasite Stage

Conesa

Sevilla

Terrón

et al. 2020

mSphere

View full text Add to dashboard Cite

Babesia is an apicomplexan parasite of significance that causes the disease known as babesiosis in domestic and wild animals and in humans worldwide. Babesia infects vertebrate hosts and reproduces asexually by a form of binary fission within erythrocytes/red blood cells (RBCs), yielding a complex pleomorphic population of intraerythrocytic parasites. Seven of them, clearly visible in human RBCs infected with Babesia divergens, are considered the main forms and named single, double, and quadruple trophozoites, paired and double paired pyriforms, tetrad or Maltese Cross, and multiparasite stage. However, these main intraerythrocytic forms coexist with RBCs infected with transient parasite combinations of unclear origin and development. In fact, little is understood about how Babesia builds this complex population during its asexual life cycle. By combining cryo-soft X-ray tomography and video microscopy, main and transitory parasites were characterized in a native whole cellular context and at nanometric resolution. The architecture and kinetics of the parasite population was observed in detail and provide additional data to the previous B. divergens asexual life cycle model that was built on light microscopy. Importantly, the process of multiplication by binary fission, involving budding, was visualized in live parasites for the first time, revealing that fundamental changes in cell shape and continuous rounds of multiplication occur as the parasites go through their asexual multiplication cycle. A four-dimensional asexual life cycle model was built highlighting the origin of several transient morphological forms that, surprisingly, intersperse in a chronological order between one main stage and the next in the cycle. IMPORTANCE Babesiosis is a disease caused by intraerythrocytic Babesia parasites, which possess many clinical features that are similar to those of malaria. This worldwide disease is increasing in frequency and geographical range and has a significant impact on human and animal health. Babesia divergens is one of the species responsible for human and cattle babesiosis causing death unless treated promptly. When B. divergens infects its vertebrate hosts, it reproduces asexually within red blood cells. During its asexual life cycle, B. divergens builds a population of numerous intraerythrocytic (IE) parasites of difficult interpretation. This complex population is largely unexplored, and we have therefore combined three- and four-dimensional imaging techniques to elucidate the origin, architecture, and kinetics of IE parasites. Unveiling the nature of these parasites has provided a vision of the B. divergens asexual cycle in unprecedented detail and is a key step to develop control strategies against babesiosis.

show abstract

TomoEED: fast edge-enhancing denoising of tomographic volumes

Abstract: Supplementary data are available at Bioinformatics online.

Cited by 18 publications

References 9 publications

In situ structural analysis of the flagellum attachment zone in Trypanosoma brucei using cryo-scanning transmission electron tomography

In situ structural analysis of the flagellum attachment zone in Trypanosoma brucei using cryo-scanning transmission electron tomography

Reliable estimation of membrane curvature for cryo-electron tomography

Four-Dimensional Characterization of the Babesia divergens Asexual Life Cycle, from the Trophozoite to the Multiparasite Stage

Contact Info

Product

Resources

About