@inproceedings{knapp_evaluation_2022,
	title = {Evaluation of tile artifact correction methods for multiphoton microscopy mosaics of whole-slide tissue sections},
	volume = {11966},
	url = {https://www.spiedigitallibrary.org/conference-proceedings-of-spie/11966/119660D/Evaluation-of-tile-artifact-correction-methods-for-multiphoton-microscopy-mosaics/10.1117/12.2609634.full},
	doi = {10.1117/12.2609634},
	abstract = {Multi-photon microscopy (MPM) is a useful biomedical imaging tool due, in part, to its capabilities of probing tissue biomarkers at high resolution and with depth-resolved capabilities. Automated MPM tile scanning allows for whole-slide image acquisition but suffers from tile-stitching artifacts that prevent accurate quantitative data analysis. We have investigated a variety of post-processing artifact correction methods using ImageJ macros and custom Python/ MATLAB code and present a quantitative and qualitative comparison of these methods using whole-slide MPM autofluorescence images of human duodenal tissue. Image quality is assessed via evaluation of artifact removal compared to the calculated mean square error (MSE), peak signal-to-noise ratio (PSNR), and structural similarity index (SSIM) of the processed image and its raw counterpart. Consideration of both quantitative and qualitative results suggest a combination of flat-field based correction and frequency filtering processing steps provide improved artifact correction when compared to each method used independently to correct for tiling artifacts of tile-scan MPM images.},
	urldate = {2022-12-03},
	booktitle = {Three-{Dimensional} and {Multidimensional} {Microscopy}: {Image} {Acquisition} and {Processing} {XXIX}},
	publisher = {SPIE},
	author = {Knapp, Thomas and Lima, Natzem and Duan, Suzann and Merchant, Juanita L. and Sawyer, Travis W.},
	month = mar,
	year = {2022},
	pages = {74--86},
}

{"_id":"7ADstZ6SB9JXfcenb","bibbaseid":"knapp-lima-duan-merchant-sawyer-evaluationoftileartifactcorrectionmethodsformultiphotonmicroscopymosaicsofwholeslidetissuesections-2022","author_short":["Knapp, T.","Lima, N.","Duan, S.","Merchant, J. L.","Sawyer, T. W."],"bibdata":{"bibtype":"inproceedings","type":"inproceedings","title":"Evaluation of tile artifact correction methods for multiphoton microscopy mosaics of whole-slide tissue sections","volume":"11966","url":"https://www.spiedigitallibrary.org/conference-proceedings-of-spie/11966/119660D/Evaluation-of-tile-artifact-correction-methods-for-multiphoton-microscopy-mosaics/10.1117/12.2609634.full","doi":"10.1117/12.2609634","abstract":"Multi-photon microscopy (MPM) is a useful biomedical imaging tool due, in part, to its capabilities of probing tissue biomarkers at high resolution and with depth-resolved capabilities. Automated MPM tile scanning allows for whole-slide image acquisition but suffers from tile-stitching artifacts that prevent accurate quantitative data analysis. We have investigated a variety of post-processing artifact correction methods using ImageJ macros and custom Python/ MATLAB code and present a quantitative and qualitative comparison of these methods using whole-slide MPM autofluorescence images of human duodenal tissue. Image quality is assessed via evaluation of artifact removal compared to the calculated mean square error (MSE), peak signal-to-noise ratio (PSNR), and structural similarity index (SSIM) of the processed image and its raw counterpart. Consideration of both quantitative and qualitative results suggest a combination of flat-field based correction and frequency filtering processing steps provide improved artifact correction when compared to each method used independently to correct for tiling artifacts of tile-scan MPM images.","urldate":"2022-12-03","booktitle":"Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XXIX","publisher":"SPIE","author":[{"propositions":[],"lastnames":["Knapp"],"firstnames":["Thomas"],"suffixes":[]},{"propositions":[],"lastnames":["Lima"],"firstnames":["Natzem"],"suffixes":[]},{"propositions":[],"lastnames":["Duan"],"firstnames":["Suzann"],"suffixes":[]},{"propositions":[],"lastnames":["Merchant"],"firstnames":["Juanita","L."],"suffixes":[]},{"propositions":[],"lastnames":["Sawyer"],"firstnames":["Travis","W."],"suffixes":[]}],"month":"March","year":"2022","pages":"74–86","bibtex":"@inproceedings{knapp_evaluation_2022,\n\ttitle = {Evaluation of tile artifact correction methods for multiphoton microscopy mosaics of whole-slide tissue sections},\n\tvolume = {11966},\n\turl = {https://www.spiedigitallibrary.org/conference-proceedings-of-spie/11966/119660D/Evaluation-of-tile-artifact-correction-methods-for-multiphoton-microscopy-mosaics/10.1117/12.2609634.full},\n\tdoi = {10.1117/12.2609634},\n\tabstract = {Multi-photon microscopy (MPM) is a useful biomedical imaging tool due, in part, to its capabilities of probing tissue biomarkers at high resolution and with depth-resolved capabilities. Automated MPM tile scanning allows for whole-slide image acquisition but suffers from tile-stitching artifacts that prevent accurate quantitative data analysis. We have investigated a variety of post-processing artifact correction methods using ImageJ macros and custom Python/ MATLAB code and present a quantitative and qualitative comparison of these methods using whole-slide MPM autofluorescence images of human duodenal tissue. Image quality is assessed via evaluation of artifact removal compared to the calculated mean square error (MSE), peak signal-to-noise ratio (PSNR), and structural similarity index (SSIM) of the processed image and its raw counterpart. Consideration of both quantitative and qualitative results suggest a combination of flat-field based correction and frequency filtering processing steps provide improved artifact correction when compared to each method used independently to correct for tiling artifacts of tile-scan MPM images.},\n\turldate = {2022-12-03},\n\tbooktitle = {Three-{Dimensional} and {Multidimensional} {Microscopy}: {Image} {Acquisition} and {Processing} {XXIX}},\n\tpublisher = {SPIE},\n\tauthor = {Knapp, Thomas and Lima, Natzem and Duan, Suzann and Merchant, Juanita L. and Sawyer, Travis W.},\n\tmonth = mar,\n\tyear = {2022},\n\tpages = {74--86},\n}\n\n","author_short":["Knapp, T.","Lima, N.","Duan, S.","Merchant, J. L.","Sawyer, T. W."],"key":"knapp_evaluation_2022","id":"knapp_evaluation_2022","bibbaseid":"knapp-lima-duan-merchant-sawyer-evaluationoftileartifactcorrectionmethodsformultiphotonmicroscopymosaicsofwholeslidetissuesections-2022","role":"author","urls":{"Paper":"https://www.spiedigitallibrary.org/conference-proceedings-of-spie/11966/119660D/Evaluation-of-tile-artifact-correction-methods-for-multiphoton-microscopy-mosaics/10.1117/12.2609634.full"},"metadata":{"authorlinks":{}},"html":""},"bibtype":"inproceedings","biburl":"https://bibbase.org/zotero/natzem","dataSources":["pa4CjeiS7oDnQDkEc"],"keywords":[],"search_terms":["evaluation","tile","artifact","correction","methods","multiphoton","microscopy","mosaics","whole","slide","tissue","sections","knapp","lima","duan","merchant","sawyer"],"title":"Evaluation of tile artifact correction methods for multiphoton microscopy mosaics of whole-slide tissue sections","year":2022}