Quantitative pixel intensity- and color-based image analysis on minimally compressed files: implications for whole-slide imaging.
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. Ho...
| Published in: | Histochemistry & Cell Biology Vol. 152; no. 1; pp. 13 - 24 |
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| Main Authors: | , , , , , |
| Format: | Journal Article |
| Published: |
Springer Nature
Jul2019
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| Online Access: | View this record in EBSCOhost |
| fields | @attributes: recordID: 1 pdfLink: plink: https://search.ebscohost.com/login.aspx?direct=true&db=ccm&AN=137419841&site=ehost-live header: @attributes: shortDbName: ccm uiTerm: 137419841 longDbName: CINAHL Complete uiTag: AN controlInfo: bkinfo: dissinfo: jinfo: jid: 09486143 NQI jtl: Histochemistry & Cell Biology issn: 09486143 maglogo: N pubinfo: dt: Jul2019 vid: 152 iid: 1 pid: 237 pub: Springer Nature place: New York, New York artinfo: ui: 137419841 10.1007/s00418-019-01783-7 137419841 ppf: 13 ppct: 11 formats: fmt: – @attributes: type: T – @attributes: type: P tig: atl: Quantitative pixel intensity- and color-based image analysis on minimally compressed files: implications for whole-slide imaging. aug: au: Taatjes, Douglas J. Bouffard, Nicole A. Barrow, Taylor Devitt, Katherine A. Gardner, Juli-Anne Braet, Filip affil: Department of Pathology and Laboratory Medicine, University of Vermont, 05405, Burlington, VT, USA sug: ab: 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. pubtype: Academic Journal doctype: Journal Article ougenre: Article language: English refInfo: holdings: @attributes: islocal: N |
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