The Spectral Pathology Lab is a research group in the Department of Pathology at the University of Illinois at Chicago led by Dr Michael J Walsh.

Please check out the website for information about the SPL research group and for contact information. The groups research is broadly focused on developing novel chemical imaging approaches towards biomedical applications.


Recent News and Developments

  • New publication in Analyst! Berisha S, Lotfollahi M, Jahanipour J, Gurcan I, Walsh MJ, Bhargava R, Nguyen H, and Mayerich D. Deep learning for FTIR histology: leveraging spatial and spectral features with convolutional neural networks. Analyst 2019. Link.
  • New publication in IEEE Transactions in Medical Imaging! Kumar N., Uppala P., Duddu K., Sreedhar H., Varma V., Guzman G., Walsh MJ., and Sethi A. IEEE Transactions in Medical Imaging. Hyperspectral Tissue Image Segmentation using Semi-Supervised NMF and Hierarchical Clustering. 2018.
  • New publication in Transplantation! "Label-free identification of antibody-mediated rejection in cardiac allograft biopsies using infrared spectroscopic imaging." Imran Uraizee*, Vishal K Varma*, Hari Sreedhar, Francesca Gambacorta, Shaiju Nazeer, Aliya Husain#, Michael J Walsh#. Transplantation 2018. In Press.
  • New publication in Analyst! Rupali Mankar,  Michael Walsh,  Rohit Bhargava,  Saurabh Prasad  and  David Mayerich " "Selecting optimal features from Fourier transform infrared spectroscopy for discrete-frequency imaging" Analyst 2018 (In Press). Link.
  • New publication in Scientific Reports! "Predicting Fibrosis Progression in Renal Transplant Recipients Using Laser-Based Infrared Spectroscopic Imaging" 2018. Link.

  • Dr Walsh has two invited talks this month at SCIX (link) and the American Society for Nephrology (link)!
  • New invited Imaging in Focus review article from my lab in the International Journal of Biochemistry and Cell Biology. "Infrared Spectroscopic Imaging: Label-Free Biochemical Analysis of Stroma and Tissue Fibrosis" 
  • Shaiju S Nazeer*, 
  • Hari Sreedhar*, 
  • Vishal K. Varma, 
  • David Martinez-Marin, 
  • Christine Massie, 
  • Michael J. Walsh (In Press). * Joint first. Link
  • Big congratulations to (now Dr.) Vishal Varma for successfully defending his PhD defense (AKA viva)! 

  • Updated lab photo!

  • Dr. Walsh has been invited to give a talk at the upcoming SCIX conference in Reno, NV (Link) and American Society for Nephrology (ASN) Annual Conference in New Orleans, LA (Link)!
  • New extended abstract published in the journal Amyloid! "Infrared spectroscopic imaging: a label free approach for the detection of amyloidosis in human tissue biopsies". Link
  • New SPIE Proceedings paper published! Hari Sreedhar, Vishal Varma, Benjamin Bird, Grace Guzman, and Michael J Walsh. 'Applications of QCL Imaging to the Advancement of Pathology'. Proc. SPIE 10140, Medical Imaging 2017: Digital Pathology, 1014004. Link.
  • Welcome to Dr. Shaiju Nazeer as a new postdoctoral researcher in the lab! 
  • Congratulations Hari Sreedhar on being selected as a James Scholar by the College of Medicine to continue his research in the Spectral Pathology Lab! 
  • New publication from my lab as an invited submission to the Prominent Young Vibrational Spectroscopists edition of Vibrational Spectroscopy - "Accounting for tissue heterogeneity in infrared spectroscopic imaging for accurate diagnosis of thyroid carcinoma subtypes". Link.
  • Congratulations Vishal Varma on being awarded the 2016/2017 CCTS Pre-doctoral Education for Clinical and Translational Scientists Fellowship!
  • Awarded UIC College of Medicine Department of Pathology Rising Star Award!

  • Paper accepted in Biomedical Optics Express!  "Infrared Spectroscopic Imaging Detects Chemical Modifications in Liver Fibrosis due to Diabetes and Disease." Hari Sreedhar, Vishal Varma, Francesca Gambacorta, Grace Guzman, and Michael J. Walsh. Now online! Link.

  • Featured on the front cover of Kidney International!  Link.              
  • Varma V, Kajdacsy-Balla A, Akkina S, Setty S, Walsh MJ. Response to Letter to Editor: Infrared spectroscopic imaging for interrogating the carbohydrate biochemistry of diabetic nephropathy progression. 2016 Kidney International (In Press).
  • Postdoctoral position open - for full consideration submit by July 1st 2016 - Link.
  • Oral and Poster accepted at SPEC2016 in Montreal, Canada. June 2016.
  • Dr. Walsh will be giving an invited talk at the Midwest Fibrosis Symposium: Molecular Mechanisms to Emerging Therapies on Monday 11 April 2016 at MATTER Suite 1230 at the Merchandise Mart (Chicago, IL). Link.
  • New paper In Press - "Using Raman spectroscopy to characterize biological materials" 
  • Holly J Butler,
  • Lorna Ashton,
  • Benjamin Bird,
  • Gianfelice Cinque,
  • Kelly Curtis,
  • Jennifer Dorney,
  • Karen Esmonde-White,
  • Nigel J Fullwood,
  • Benjamin Gardner,
  • Pierre L Martin-Hirsch,
  • Michael J Walsh,
  • Martin R McAinsh,
  • Nicholas Stone
  • Francis L Martin. Nature Protocols 2016 (In Press). Link.

  • New paper from the lab is In Press - "A label-free approach by infrared spectroscopic imaging for interrogating the biochemistry of diabetic nephropathy progression". Vishal K. Varma, Andre Kajdacsy-Balla, Sanjeev K. Akkina, Suman Setty and Michael J. Walsh. Kidney International 2016 (In Press). Link.
  • Three abstracts accepted for two posters and an oral presentation at USCAP 2016 in Seattle, WA.


  • The University of Illinois at Chicago Inaugural Transplant Day was a big success. We thank all the attendees and speakers for such a stimulating day!
  • Abstract submission for the University of Illinois at Chicago Inaugural Transplant Day is now live. UIC Transplant Day
  • Congratulations to Vishal Varma for winning a poster award at the SCIX 2015 conference. Great job!
  • New academic year, new lab photo! 

  • New article from the lab published in the Sept '15 issue of Biophotonics! "Using QCLs for MIR-Based Spectral Imaging — Applications in Tissue Pathology". Link.
  • I (along with Dr. Suman Setty and Dr. Grace Guzman) am organizing a Transplant Symposium at UIC on November 19th. Please save the date! Final list of speakers and abstract submission for posters will be available on this website in the next week.

  • The lab has received funding from the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) for the project "Early detection of diabetic nephropathy in kidney transplants by chemical imaging approaches".
  • The lab will be attending the SCIX conference in September (Providence, Rhode Island) to present to invited oral presentations and two posters. More details to follow.
  • Congratulations to Hari Sreedhar and Amruta Bhatt who are heading to medical school and Peter Nguyen who is heading to Johns Hopkins! 
  • Hari Sreedhar has had a paper accepted in the peer-reviewed the UIC Bioengineering Student Journal entitled, "High-Definition Infrared Spectroscopic Tissue Imaging: Potential applications in Pathology". Link.
  • 'Stain-less staining for computed histopathology'. Mayerich D, Walsh MJ, Kajdacsy-Balla A, Ray PS, Hewitt SM, Bhargava R. Technology 03 27(2015). Link
  • Dr. Walsh will be an invited speaker at the Society for Applied Spectroscopy Cleveland section on 22nd April 2015 and at the Beckman Institute in Champaign IL for the Illinois iOptics seminar series on the 24th April 2015. Details can be found at the respective websites.
  • Awarded Chicago Biomedical Consortium Catalyst award (Co-PI with Aliya Husain, University of Chicago, Department of Pathology). More details.
  • Congratulations to Vishal Varma for being awarded a Association for Pathology Informatics (API) travel grant to attend the Pathology Informatics 2015 conference in Pittsburgh!
  • 'Improving Prediction of Prostate Cancer Recurrence using Chemical Imaging' Kwak J, Kajdacsy-Balla A, Macias V, Walsh MJ, Sinha S, Bhargava R. Scientific Reports 5 (2015). Link.
  • Journal of Visualized Experiments (JoVE) article - "High-definition Fourier Transform Infrared (FT-IR) Spectroscopic Imaging of Human Tissue Sections towards Improving Pathology" is now online and Open Access - Link.
Jove Article

  • 2 year anniversary of the Spectral Pathology Lab!

  • Two posters from the group will be presented at the United States and Canadian Academy of Pathology (USCAP) meeting in the Monday PM Techniques session - "IR Spectroscopic Imaging of Heart Transplant Biopsies Towards Improving Detection of Antibody Mediated Rejection" (#294) and "Investigating the Progression of Liver Disease To Hepatocellular Carcinoma Using Label-Free Chemical Imaging" (#283).
  • Invited talk at Pittcon - "Improving Prediction of Organ Transplant Outcome Using FT-IR Spectroscopic Imaging" at 8.35am 9th March in room 274, in the Advances in Clincal Infrared and Raman Spectroscopy session (New Orleans Morial Convention Center.
  • Honors class "Advances in Interdisciplinary Research: Bridging the gap between Engineering and Medicine" will now have all material hosted on Blackboard. The class has reached its cap however please email me if and I can request with the Honors college for additional seats to be made available.
  • Coverage and photos of the Megger's award certificate presentation at SCIX 2014 in the December edition of the Society for Applied Spectroscopy - Link


  • Photos of two undergraduates from the lab (Hari and Ben) receiving awards at SCIX 2014 highlighted in the November edition of the Society for Applied Spectroscopy - Link