Journal: bioRxiv

Article Title: CellBinDB: A Large-Scale Multimodal Annotated Dataset for Cell Segmentation with Benchmarking of Universal Models

doi: 10.1101/2024.11.20.619750

Figure Lengend Snippet: a, Distribution of staining types in CellBinDB. b, Distribution of tissue types in CellBinDB, where tissue types with less than 10 samples are included in other, for details, see supplementary table 1. c, Examples of CellBinDB images and their two types of (semantic and instance) ground truth annotations, with 10 μ m scale bar from left to right columns 1, 2: ssDNA, columns 3, 4: DAPI, columns 5, 6: H&E, columns 7, 8: mIF, column 9: 10x Genomics DAPI, column 10: 10x Genomics H&E. The first row is the original microscope image, followed by the semantic annotation mask and instance annotation mask. d, Scatter plot of t-SNE demonstrates the diverse spread of data by different staining types and sources. e, Scatter plot of t-SNE demonstrates the diversity of CellBinDB compared to previous datasets. f, The number of manual and semi-automatic annotations in CellBinDB. g, The dataset annotation process includes four steps: 1.model annotation, 2.annotation team modification/re-annotation(depends on the model annotation results), 3.expert review, go to the next step if the annotations are correct, otherwise return to the second step for modification, 4. add the original image and the two masks to the dataset.

Article Snippet: WSIs are generated by 1. a STOmics Microscope Go Optical equipped with Scanner Version 1.2.2, using 10×/0.75 NA and 20X/0.5 NA objective and Go Optical Scanner Ximea Mc124 for grayscale images and Go Optical Scanner Ximea Mc050 for RGB images.

Techniques: Staining, Microscopy, Modification

Journal: Scientific Reports

Article Title: Real-time monitoring of the dynamics and interactions of bacteria and the early-stage formation of biofilms

doi: 10.1038/s41598-022-22669-0

Figure Lengend Snippet: Comparison between the same E. coli bacteria population imaged with an inverted optical microscope in caustics mode (top) and fluorescence mode (bottom). E. coli bacteria were stained with the fluorescent dyes SYTO9 and propidium iodide (PI) from the LIVE/DEAD BacLight kit. There are no significant differences between the two imaging techniques. The three bacteria highlighted by the black arrows in the caustics image are not at the surface and have been captured when aligned perpendicularly to the surface during their random diffusion, resulting in an almost spherical optical signature.

Article Snippet: Bacterial dynamics and interactions were monitored in a standard optical inverted microscope (Axio Observer.Z1 m, Carl Zeiss), mounted on antivibration feet (VIBe, Newport) to isolate the sample from the environment, using 60 μl of bacteria solution in a deep cavity (250 ± 10 μm in depth) in microscopy slides.

Techniques: Comparison, Bacteria, Microscopy, Fluorescence, Staining, Imaging, Diffusion-based Assay

Journal: Scientific Reports

Article Title: Real-time monitoring of the dynamics and interactions of bacteria and the early-stage formation of biofilms

doi: 10.1038/s41598-022-22669-0

Figure Lengend Snippet: Photograph of the optical signature generated by an E. coli bacterium taken with the optical inverted microscope used in this work set-up for: ( a ) caustics mode; ( b ) brightfield mode.

Article Snippet: Bacterial dynamics and interactions were monitored in a standard optical inverted microscope (Axio Observer.Z1 m, Carl Zeiss), mounted on antivibration feet (VIBe, Newport) to isolate the sample from the environment, using 60 μl of bacteria solution in a deep cavity (250 ± 10 μm in depth) in microscopy slides.

Techniques: Generated, Inverted Microscopy

Journal: Scientific Reports

Article Title: Real-time monitoring of the dynamics and interactions of bacteria and the early-stage formation of biofilms

doi: 10.1038/s41598-022-22669-0

Figure Lengend Snippet: E. coli bacteria stained with trypan blue and statically attached to a BKC surface imaged with an inverted optical microscope in caustics mode ( a ) and fluorescence mode ( b ).

Article Snippet: Bacterial dynamics and interactions were monitored in a standard optical inverted microscope (Axio Observer.Z1 m, Carl Zeiss), mounted on antivibration feet (VIBe, Newport) to isolate the sample from the environment, using 60 μl of bacteria solution in a deep cavity (250 ± 10 μm in depth) in microscopy slides.

Techniques: Bacteria, Staining, Microscopy, Fluorescence