Computer Assisted Segmentation Tool: A Machine Learning Based Image Segmenting Tool for TrakEM2

Tropea, Augustus N.; Valerio, Janey L.; Camerino, Michael J.; Hix, Josh; Pecor, Emmalee; Fuerst, Peter G.; Long, Sean P.

doi:10.1007/978-3-319-59575-7_22

Cited by 3 publications

(2 citation statements)

References 12 publications

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“…These projects teach students essential research skills such as working with NIH's imageJ software and downstream statistical analysis and benefits the research team by essential data sets to studies (Camerino et al, 2020; de Andrade et al, 2014; Li, Mitchell, et al, 2016; Li, Woodfin, et al, 2016; Simmons et al, 2020; Tropea et al, 2017). Of the remote students we have worked with 91% graduated within starting college (Table 1).…”

Section: Resultsmentioning

confidence: 99%

Student remote and distance research in neuroanatomy: Mapping Dscaml1 expression with a LacZ gene trap in mouse brain

Clemons

Flores

Black

et al. 2022

Anat Histol Embryol

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Undergraduate student engagement in research increases retention and degree completion, especially for students who are underrepresented in science. Several approaches have been adopted to increase research opportunities including curriculum based undergraduate research opportunities (CUREs), in which research is embedded into course content. Here we report on efforts to tackle a different challenge: providing research opportunities to students engaged in remote learning or who are learning at satellite campuses or community colleges with limited research infrastructure. In our project we engaged students learning remotely or at regional centers to map gene expression in the mouse brain. In this project we mapped expression of the Down syndrome cell adhesion molecule like 1 (Dscaml1) gene in mouse brain using a LacZ expression reporter line. Identifying where Dscaml1 is expressed in the brain is an important next step in determining if its roles in development and function in the retina are conserved in the rest of the brain. Students working remotely reconstruct brain montages and annotated Dscaml1 expression in the brain of mice carrying one or two copies of the gene trap. We built on these findings by further characterizing Dscaml1 expression in inhibitory neurons of the visual pathway. These results build on and extend previous findings and demonstrate the utility of including distance learners in an active research group for both the student learners and the research team. We conclude with best practices we have developed based on this and other distance learner focused projects.

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Section: Resultsmentioning

confidence: 99%

Student remote and distance research in neuroanatomy: Mapping Dscaml1 expression with a LacZ gene trap in mouse brain

Clemons

Flores

Black

et al. 2022

Anat Histol Embryol

Self Cite

View full text Add to dashboard Cite

show abstract

“…Fluorescence and differential interference contrast (DIC) images were obtained using a Leica DM6B microscope. The whole retina was photographed by sequentially taking images from different areas and later those photographs were stitched together using TrackEM2 in Image J (Schindelin et al, 2012; Tropea et al, 2017).…”

Section: Methodsmentioning

confidence: 99%

Diversity in visual sensitivity across Neotropical cichlid fishes via differential expression and intraretinal variation of opsin genes

et al. 2021

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The visual system of vertebrates has greatly contributed to our understanding of how different molecular mechanisms shape adaptive phenotypic diversity. Extensive work on African cichlid fishes has shown how variation in opsin gene expression mediates diversification as well as convergent evolution in colour vision. This trait has received less attention in Neotropical cichlids, the sister lineage to African cichlids, but the work done so far led to the conclusion that colour vision is much less variable in Neotropical species. However, as only few taxa have been investigated and as recent work found contradicting patterns, the diversity in meotropical cichlids might be greatly underestimated. Here, we survey patterns of opsin gene expression in 35 representative species of Neotropical cichlids, revealing much more variation than previously known. This diversity can be attributed to two main mechanisms: (i) differential expression of the blue‐sensitive sws2a, the green‐sensitive rh2a, and the red‐sensitive lws opsin genes, and (ii) simultaneous expression of up to five opsin genes, instead of only three as commonly found, in a striking dorsoventral pattern across the retina. This intraretinal variation in opsin genes expression results in steep gradients in visual sensitivity that may represent a convergent adaptation to clear waters with broad light environments. These results highlight the role and flexibility of gene expression in generating adaptive phenotypic diversification.

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Computer‐Assisted Image Analysis of the Distribution and Intensity of Reactive Oxygen Species Accumulation in Plant Leaves

Sekulska‐Nalewajko

Gocławski

Kużniak

2019

Reactive Oxygen, Nitrogen and Sulfur Species in Plants

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Computer Assisted Segmentation Tool: A Machine Learning Based Image Segmenting Tool for TrakEM2

Cited by 3 publications

References 12 publications

Student remote and distance research in neuroanatomy: Mapping Dscaml1 expression with a LacZ gene trap in mouse brain

Student remote and distance research in neuroanatomy: Mapping Dscaml1 expression with a LacZ gene trap in mouse brain

Diversity in visual sensitivity across Neotropical cichlid fishes via differential expression and intraretinal variation of opsin genes

Computer‐Assisted Image Analysis of the Distribution and Intensity of Reactive Oxygen Species Accumulation in Plant Leaves

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