Evidence map›Paper›PMID 36463932›Full record

ArticleJournal of molecular biology2023

BASIN: A Semi-automatic Workflow, with Machine Learning Segmentation, for Objective Statistical Analysis of Biomedical and Biofilm Image Datasets.

Timothy W Hartman, Evgeni Radichev, Hafiz Munsub Ali, Mathew Olakunle Alaba, Mariah Hoffman, Gideon Kassa, Rajesh Sani, Venkata Gadhamshetty, Shankarachary Ragi, Shanta M Messerli and 5 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of molecular biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

  1. Article
  2. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

15 authors.

Timothy W HartmanBiomedical Engineering Department, University of South Dakota Sioux Falls, 4800 N Career Avenue, Sioux Falls, SD 57107, United States.
Evgeni RadichevBiomedical Engineering Department, University of South Dakota Sioux Falls, 4800 N Career Avenue, Sioux Falls, SD 57107, United States.
Hafiz Munsub AliBiomedical Engineering Department, University of South Dakota Sioux Falls, 4800 N Career Avenue, Sioux Falls, SD 57107, United States.
Mathew Olakunle AlabaBiomedical Engineering Department, University of South Dakota Sioux Falls, 4800 N Career Avenue, Sioux Falls, SD 57107, United States.
Mariah HoffmanBiomedical Engineering Department, University of South Dakota Sioux Falls, 4800 N Career Avenue, Sioux Falls, SD 57107, United States.
Gideon KassaBiomedical Engineering Department, University of South Dakota Sioux Falls, 4800 N Career Avenue, Sioux Falls, SD 57107, United States.
Rajesh SaniChemical and Biological Engineering Department, South Dakota School of Mines and Technology, 501 E St. Joseph Street, Rapid City, SD 57701, United States.
Venkata GadhamshettyCivil and Environmental Engineering Department, South Dakota School of Mines and Technology, 501 E St. Joseph Street, Rapid City, SD 57701, United States.
Shankarachary RagiElectrical Engineering Department, South Dakota School of Mines and Technology, 501 E St. Joseph Street, Rapid City, SD 57701, United States.
Shanta M MesserliBiomedical Engineering Department, University of South Dakota Sioux Falls, 4800 N Career Avenue, Sioux Falls, SD 57107, United States; Cancer Biology and Immunotherapies Group, Sanford Research, 2301 E 60(th) Street North, Sioux Falls, SD 57104, United States; Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57006, United States.
Pilar de la PuenteCancer Biology and Immunotherapies Group, Sanford Research, 2301 E 60(th) Street North, Sioux Falls, SD 57104, United States.
Eric S SandhurstBiomedical Engineering Department, University of South Dakota Sioux Falls, 4800 N Career Avenue, Sioux Falls, SD 57107, United States.
Tuyen DoBiomedical Engineering Department, University of South Dakota Sioux Falls, 4800 N Career Avenue, Sioux Falls, SD 57107, United States.
Carol LushboughBiomedical Engineering Department, University of South Dakota Sioux Falls, 4800 N Career Avenue, Sioux Falls, SD 57107, United States.
Etienne Z GnimpiebaBiomedical Engineering Department, University of South Dakota Sioux Falls, 4800 N Career Avenue, Sioux Falls, SD 57107, United States. Electronic address: Etienne.Gnimpieba@usd.edu.

Funding

Wichozani-A Healthy Lifestyle for Rural American Indian Youth through Cultural and Physical Activities: A Community-Based Participatory Research StudyP20GM103443 · NIGMS · UNIVERSITY OF SOUTH DAKOTA · PI Ryan Michael Johnson · 2012 to 2026
$58.1M
WESTCORE DNA SEQUENCING AND GENOTYPING CORE FACILITYP20RR016479 · NCRR · UNIVERSITY OF SOUTH DAKOTA · PI EICHLER, BARRETT · 2001 to 2011
$32.2M
NCRR NIH HHS P20 RR016479NIGMS NIH HHS P20 GM103443
6 · The paper itself

Abstract

Micrograph comparison remains useful in bioscience. This technology provides researchers with a quick snapshot of experimental conditions. But sometimes a two- condition comparison relies on researchers' eyes to draw conclusions. Our Bioimage Analysis, Statistic, and Comparison (BASIN) software provides an objective and reproducible comparison leveraging inferential statistics to bridge image data with other modalities. Users have access to machine learning-based object segmentation. BASIN provides several data points such as images' object counts, intensities, and areas. Hypothesis testing may also be performed. To improve BASIN's accessibility, we implemented it using R Shiny and provided both an online and offline version. We used BASIN to process 498 image pairs involving five bioscience topics. Our framework supported either direct claims or extrapolations 57% of the time. Analysis results were manually curated to determine BASIN's accuracy which was shown to be 78%. Additionally, each BASIN version's initial release shows an average 82% FAIR compliance score.

Indexed as

BiofilmsBiological Science DisciplinesImage Processing, Computer-AssistedMachine LearningSoftwareDatasets as TopicWorkflowbiofilmcancerFAIRimage comparisonmachine learningMicrobemicroscope imagingsegmentationstatistical analysis

Identifiers

PMID36463932
PMCPMC10280363

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.