A convolutional neural network for segmentation of yeast cells without manual training annotations

MOTIVATION: Single-cell time-lapse microscopy is a ubiquitous tool for studying the dynamics of complex cellular processes. While imaging can be automated to generate very large volumes of data, the processing of the resulting movies to extract high-quality single-cell information remains a challenging task. The development of software tools that automatically identify and track cells is essential for realizing the full potential of time-lapse microscopy data. Convolutional neural networks (CNNs) are ideally suited for such applications, but require great amounts of manually annotated data for training, a time-consuming and tedious process. RESULTS: We developed a new approach to CNN training for yeast cell segmentation based on synthetic data and present (i) a software tool for the generation of synthetic images mimicking brightfield images of budding yeast cells and (ii) a convolutional neural network (Mask R-CNN) for yeast segmentation that was trained on a fully synthetic dataset. The Mask R-CNN performed excellently on segmenting actual microscopy images of budding yeast cells, and a density-based spatial clustering algorithm (DBSCAN) was able to track the detected cells across the frames of microscopy movies. Our synthetic data creation tool completely bypassed the laborious generation of manually annotated training datasets, and can be easily adjusted to produce images with many different features. The incorporation of synthetic data creation into the development pipeline of CNN-based tools for budding yeast microscopy is a critical step toward the generation of more powerful, widely applicable and user-friendly image processing tools for this microorganism. AVAILABILITY AND IMPLEMENTATION: The synthetic data generation code can be found at https://github.com/prhbrt/synthetic-yeast-cells. The Mask R-CNN as well as the tuning and benchmarking scripts can be found at https://github.com/ymzayek/yeastcells-detection-maskrcnn. We also provide Google Colab scripts that reproduce all the results of this work. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online

Generation of maghemite nanocrystals from iron–sulfur centres

Iron oxide nano-crystals 0.1–1.1 μm in diameter were generated on sulfur-doped amorphous carbon surfaces by electron beam irradiation of the novel 13e− high-spin complex [Fe(4-methyl-1,2-benzenedithiolate)2][NHEt3] encapsulated in a triblock copolymer. Possible relevance to iron nano-mineralization from Fe–S ferredoxin proteins and iron dysregulation in neurological disorders is discussed. Graphical abstract: Generation of maghemite nanocrystals from iron–sulfur centres Iron is an essential element for mammals and, amongst many other functions, plays an important role in the human brain.1 Recent research has indicated a strong association between iron dysregulation and Alzheimer's disease (AD), although it is unknown how the chemical and magnetic state of iron is linked to AD pathogenesis.2–4 Reports from Collingwood et al., and Dobson et al., for example, have shown the presence of iron oxide as the mixed oxidation state mineral, magnetite (Fe3O4) in AD tissue, a possible source of redox-active iron, but it remains unclear how this kind of iron mineral forms in the tissue.5,6 These unsolved and important questions have led us to consider how atomic resolution microscopy might provide new insight into nanoscale iron mineralization. Recently we reported methodology for studies of the nano-mineralisation of osmium, gold, ruthenium and iridium from their respective 1,2-dicarba-closo-dodecarborane-1,2-dithiolate complexes encapsulated in polymer micelles upon electron beam irradiation.7–9 Here we report the synthesis and characterization of the novel 13e− iron(iii) complex [Fe(4-methyl-1,2-benzenedithiolate)2][NHEt3] (1), containing Fe–S bonds analogous to those in the ubiquitous iron–sulfur ferredoxin proteins. Importantly, recent research has indicated a strong relationship between neurodegenerative disorders and defective Fe–S clusters.10,11 We have characterized complex 1 using Mössbauer, Raman and far-infra red spectroscopy, and investigated the generation of iron nanocrystals from 1 encapsulated in a poly(ethylene glycol)-block-poly(propylene glycol)-block-poly(ethylene glycol) polymer (Scheme 1) by electron beam irradiation, and used electron energy-loss spectra (EELS) to identify the oxidation state of iron and its coordination environment in the nanocrystals

Iron(II) Complexes of Chiral Tridentate Nitrogen Donors and their Application in Catalytic Hydrosilylation Reactions

Enantiomerically pure, C2-symmetric 2,6-bis(pyrazol-3-yl) pyridine ligands were obtained by treatment of diethyl-2,6-pyridinedicarbonate with (1R,4R)-(+)-camphor in the presence of NaH followed by ring closure with hydrazine. After twofold N-alkylation at the pyrazole rings, the addition of iron(II) chloride led to the according pentacoordinate dichloridoiron(II) complexes. All intermediates of the ligand synthesis, the ligands bearing NCH3 and NCH2C6H5 groups and the derived iron(II) complexes were structurally characterized by means of X-ray structure analysis. In-situ reaction with iron(II) carboxylates resulted in the formation of iron(II) carboxylate complexes, which turned out to be highly active in the hydrosilylation of acetophenone. However, even at room temperature, the enantiomeric excess of the product 1-phenylethanol is poor. 57Fe Mössbauer spectroscopy gave an insight into the species formed during catalysis

Vibrational properties of the mononuclear Fe[HBpz3_3]2_2 spin crossover complex

Within this work, we report the results of nuclear inelastic scattering experiments of the low-spin phase of the iron(II) mononuclear SCO complex Fe[HBpz$_3$]$_2$ and density functional theory based calculations performed on a model molecule of the complex. We show that the calculated partial density of vibrational states based on the structure of a single iron(II) center which is linked by three pyrazole rings to borat is in good accordance with the experimentally obtained $^{57}$Fe-pDOS and assign the molecular vibrations to the prominent optical phonons

Vibrational properties of the mononuclear Fe[HBpz3]2 spin crossover complex

Within this work, we report the results of nuclear inelastic scattering experiments of the low-spin phase of the iron(II) mononuclear SCO complex Fe[HBpz3]2 and density functional theory based calculations performed on a model molecule of the complex. We show that the calculated partial density of vibrational states based on the structure of a single iron(II) center which is linked by three pyrazole rings to borat is in good accordance with the experimentally obtained 57Fe-pDOS and assign the molecular vibrations to the prominent optical phonons

Preparation and characterization of spin crossover thin solid films

Iron(II) spin crossover complexes display a reversible transition from low-spin (LS) state to high-spin (HS) state by e.g. variation of temperature, pressure or by irradiation with light. Therefore, these systems are promising candidates for information storage materials. In view of practical device applications thin films of these materials are needed. The SCO-compound [Fe(Htrz)2(trz)] (BF4) (1) switches between the LS and the HS state with a 50 K wide thermal hysteresis loop above room temperature. We have prepared thin films of 1 on a SiO2 substrate by spin coating. The spin states of the films have been characterized by Mössbauer spectroscopy in reflection mode using a MIMOS II spectrometer. A low quadrupole splitting (LS state) at 300 K and a high quadrupole splitting (HS state) at 400 K were found for the film, as well as for bulk powder of 1. This confirms that a spin crossover occurs above room temperature. Furthermore, synchrotron based nuclear resonance scattering measurements from 80 K to 400 K indicate that the hyperfine parameters are similar to those of the bulk powder of 1. DFT calculations reproduce the experimentally determined Fe-vibrational density of states of the bulk and of the thin film sample of 1. These results indicate that a higher fraction of HS Fe atoms is present in the film of 1. Therefore, we conclude different SCO properties of the thin film and the bulk material of 1

Quality or Quantity? How Structural Parameters Affect Catalytic Activity of Iron Oxides for CO Oxidation

The replacement of noble metal catalysts by abundant iron as an active compound in CO oxidation is of ecologic and economic interest. However, improvement of their catalytic performance to the same level as state-of-the-art noble metal catalysts requires an in depth understanding of their working principle on an atomic level. As a contribution to this aim, a series of iron oxide catalysts with varying Fe loadings from 1 to 20 wt% immobilized on a γ-Al2O3 support is presented here, and a multidimensional structure–activity correlation is established. The CO oxidation activity is correlated to structural details obtained by various spectroscopic, diffraction, and microscopic methods, such as PXRD, PDF analysis, DRUVS, Mössbauer spectroscopy, STEM-EDX, and XAS. Low Fe loadings lead to less agglomerated but high percentual amounts of isolated, tetrahedrally coordinated iron oxide species, while the absolute amount of isolated species reaches its maximum at high Fe loadings. Consequently, the highest CO oxidation activity in terms of turnover frequencies can be correlated to small, finely dispersed iron oxide species with a large amount of tetrahedrally oxygen coordinated iron sites, while the overall amount of isolated iron oxide species correlates with a lower light-off temperature