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TMAJ specifications

Information


Unique identifier OMICS_00823
Name TMAJ
Alternative name Tissue MicroArray J
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Helen Fedor

TMAJ citations

 (4)
library_books

PTEN loss detection in prostate cancer: comparison of PTEN immunohistochemistry and PTEN FISH in a large retrospective prostatectomy cohort

2017
Oncotarget
PMCID: 5630353
PMID: 29029453
DOI: 10.18632/oncotarget.19217

[…] After staining for PTEN, all TMAs were scanned at 20x magnification (Aperio, Leica Microsystems, Buffalo Grove, IL) and segmented into TMAJ for scoring (http://tmaj.pathology.jhmi.edu/). PTEN protein status was blindly and independently scored by a trained pathologist (TLL) using a previously validated scoring system (Figure ). A tis […]

library_books

Analytic Validation of a Clinical Grade PTEN Immunohistochemistry Assay in Prostate Cancer by Comparison to PTEN FISH

2016
PMCID: 4967011
PMID: 27174589
DOI: 10.1038/modpathol.2016.88

[…] After staining for PTEN, all tissue microarrays were scanned at 20× magnification (Aperio, Leica Microsystems, Buffalo Grove, IL) and segmented into TMAJ for scoring (http://tmaj.pathology.jhmi.edu/). PTEN protein status was blindly and independently scored by two trained pathologists (TLL and CLM) using a previously validated scoring system (see […]

library_books

PTEN loss and chromosome 8 alterations in Gleason grade 3 prostate cancer cores predicts the presence of un sampled grade 4 tumor: implications for Active Surveillance

2016
PMCID: 4925272
PMID: 27080984
DOI: 10.1038/modpathol.2016.63

[…] gnaling Technologies). Tissue microarray slides were scanned using the Aperio ScanScope® CS virtual slide scanner (Aperio, Vista, CA) and composite tissue microarray core images were viewed using the TMAJ software package (http://tmaj.pathology.jhmi.edu). Scoring of PTEN expression in tumor cells was performed by 2 pathologists (ADM and BG), blinded with respect to FISH results, pathologic stage, […]

library_books

Expression pattern of tumour associated antigens in hepatocellular carcinoma: association with immune infiltration and disease progression

2013
Br J Cancer
PMCID: 3749565
PMID: 23868000
DOI: 10.1038/bjc.2013.390

[…] All TMA cores were screened and evaluated with a computerised image analysis platform constructed using the TMAJ Image application (http://tmaj.pathology.jhmi.edu). The expression of each antigen was scored according to the proportion of expression, as previously described ().We initially investigated eight […]

Citations

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TMAJ institution(s)
Department of Biostatistics, School of Public Health, University of California, Los Angeles, CA, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA; Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA; Department of Pathology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA

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