Evidence map›Paper›PMID 30982111›Full record

ArticleHistochemistry and cell biology2019

Quantitative pixel intensity- and color-based image analysis on minimally compressed files: implications for whole-slide imaging.

Douglas J Taatjes, Nicole A Bouffard, Taylor Barrow, Katherine A Devitt, Juli-Anne Gardner, Filip Braet

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Article in Histochemistry and cell biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing 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

3 citing papers in PubMed.

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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

6 authors.

Douglas J TaatjesDepartment of Pathology and Laboratory Medicine, University of Vermont, Burlington, VT, 05405, USA. Douglas.taatjes@med.uvm.edu.ORCID http://orcid.org/0000-0003-1903-983X
Nicole A BouffardDepartment of Pathology and Laboratory Medicine, University of Vermont, Burlington, VT, 05405, USA.
Taylor BarrowDepartment of Pathology and Laboratory Medicine, University of Vermont, Burlington, VT, 05405, USA.
Katherine A DevittDepartment of Pathology and Laboratory Medicine, University of Vermont, Burlington, VT, 05405, USA.
Juli-Anne GardnerDepartment of Pathology and Laboratory Medicine, University of Vermont, Burlington, VT, 05405, USA.
Filip BraetAustralian Center for Microscopy and Microanalysis, The University of Sydney, Sydney, NSW, 2006, Australia.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Current best practice in the quantitative analysis of microscopy images dictates that image files should be saved in a lossless format such as TIFF. Use of lossy files, including those processed with the JPEG algorithm, is highly discouraged due to effects of compression on pixel characteristics. However, with the growing popularity of whole-slide imaging (WSI) and its attendant large file sizes, compressed image files are becoming more prevelent. This prompted us to perform a color-based quantitative pixel analysis of minimally compressed WSI images. Sections from three tissues stained with one of three reagents representing the colors blue (hematoxylin), red (Oil-Red-O), and brown (immunoperoxidase) were scanned with a whole slide imager in triplicate at 20x, 40x, and 63x magnifications. The resulting files were in the form of a BigTIFF with a JPEG compression automatically applied during acquisition. Images were imported into analysis software, six regions of interest were applied to various morphological locations, and the areas assessed for the color of interest. Whereas the number of designated weakly or strongly positive pixels was variable across the triplicate scans for the individual regions of interest, the total number of positive pixels was consistent. These results suggest that total positivity for a specific color representing a histochemical or immunohistochemical stain can be adequately quantitated on compressed images, but degrees of positivity (e.g., weak vs. strong) may not be as reliable. However, it is important to assess individual whole-slide imagers, file compression level and algorithm, and analysis software for reproducibility.

Indexed as

ColorData CompressionAlgorithmsAzo CompoundsHematoxylinHumansPeroxidaseAzo CompoundsHematoxylinoil red OPeroxidaseBigTiffImage analysisImage compressionImage dataImage focusWhole-slide imaging

Identifiers

PMID30982111

What OpenQuestion holds

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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.