Annual Newsletter

 Ndiif Newsletter

This newsletter summarizes current capabilities and highlights usage trends to date for 2021. The NDIIF operates as a recharge facility and revises user fees every July 1.

Questions about NDIIF policies should be directed to the Director or any member of the steering committee. For technical and scheduling questions, see the relevant NDIIF staff members listed throughout the website. 


Professor Bradley Smith, Director of NDIIF

Fall 2021

NDIIF News Brief
  1. Electron Microscopy and Optical Microscopy Obtain New Imaging Instruments: A Thermo Fisher Spectra 300 TEM microscope was purchase to replace the Titan TEM instrument.  The new Spectra 300 with advanced resolution also includes an EELS K3 camera and sophisticated 3D tomography data analysis software package making this a unique and versatile instrument for advancing numerous research fields of study.  The Bruker Luxendo MuVi SPIM light sheet microscope was also added to the NDIIF suite of instruments. This instrument uses innovative photon illumination techniques that can accommodate a variety of samples.
  2. NDIIF Awards for Best Imaging Publications in 2020: 
      • The Best Electron Microscopy Imaging Publication Award for 2020 was awarded to Trung Nguyen, a graduate student with Professor Mayland Chang in the Department of Chemistry and Biochemistry.
      • The Best Biological Imaging Publication Award for 2020 was awarded to Meng Jia, a graduate student with Professor David Hyde in the Department of Biological Sciences. 
      • The Best Artisitc Image Award for 2020 was awarded to Hunter Ford, a graduate student with Professor Jennifer Schaefer in the Department of Chemical and Biomolecular Engineerging.
    • Image submission for Best Imaging Publication Award in 2021 is open now and will end mid-March, 2022. 
  3. CTSI Core Facility: Affiliation with CTSI as a core research facility was renewed. For more information please visit:

Funding opportunities and grants are continually available through CTSI.  Please inquire for further information.  NDIIF staff is available to assist in budget preparation and to develop scope of work.

  1. Advanced Electron Microscopy Core: a tissue processing station for biological and soft material EM sample preparation was purchased simplifying and streamlining the current methods of room temperature embedding and sectioning of EM samples.  Currently, the NDIIF processes close to a dozen biological and soft material samples a month using this new instrument and is seeing a steady increase in usage and productivity as well as optimized image data outcomes.
  2. Optical Microscopy Core: IMARIS is a widely used tool for multiple facets of data analysis within the field of microscopy and can be used as a remote tool for users located on and off the Notre Dame campus. An updated version of this software was just recently installed and can be accessed remotely for data analysis needs.

Established in 2008, the NDIIF provides an integrated suite of sophisticated microscopes and imaging stations that enable the expert users to attack the most complex modern research problems and, equally important, the resident professional staff (technicians and research specialists) to guide the non-expert users


Advanced Microscopy                  Optical Microscopy                         Histology                             InVivo Imaging

Feature Stories

Self-discharge of magnesium–sulfur batteries leads to active material loss and poor shelf life.

Hunter O. Ford, Emily S. Doyle, Peng He, William C. Boggess, Allen G. Oliver, Tianpin Wu, George E. Sterbinsky and Jennifer L. Schaefer

Citation: Journal of Energy and Environmental Science (2020); doi:

Magnesium-sulfur batteries represent a next-generation energy storage platform with substantially higher theoretical energy density than current commercial batteries. Until this publication, there had been no direct investigations of the tendency of Mg-S batteries to undergo self-discharge. We have found that even when the battery is not being used, a series of chemical processes leading to loss of capacity occur, the results of which are severe. It was identified that active material precipitates as a solid magnesium polysulfide compound, a previously undescribed phenomenon.

Hunterford Self Discharge Of Mg S Batteries Figure Hunter Ford 1

This precipitation effect results in irreversible capacity loss, a serious concern for shelf-life. The use of the scanning electron microscope (SEM) coupled with energy dispersive x-ray spectroscopy (EDX), was instrumental to this discovery. Because of the results from the SEM-EDX, showing that the deposits contain large amounts of Mg, O, and S, we were able to get allocated beamtime at the Advanced Photon Source at the Argonne National Lab to irrefutably confirm the product as a solid magnesium polysulfide. Without NDIIF and the SEM-EDX instrumentation, this hurdle facing Mg-S batteries could not have been uncovered by our group. We hope identifying the existence of this challenge is the first step to overcoming it and pushing this technology forward. 



Discovery of a Potent Picolinamide Antibacterial Active against Clostridioides difficile

Enrico Speri, Jeshina Janardhanan, Cesar Masitas, Valerie A. Schroeder, Elena Lastochkin, William R. Wolter, Jed F. Fisher, Shahriar Mobashery*, and Mayland Chang

ACS Infectious Diseases | (2020) 6:2362-2368 | DOI:10.1021/acsinfecdis.0c00479

Clostridioides difficile is a Gram-positive, anaerobic, spore-forming bacterium that is currently designated as an urgent health problem causing life-threatening diarrhea. The disruption of the normal gut flora due to the use of broad-spectrum antibiotics facilitates the colonization and proliferation of C.difficile in the large intestine. Several antimicrobial agents have been reported recently against C. difficile. Major challenges that have not been overcome for these agents are disruption of normal gut flora, the development of resistance, and a failure to reduce recurrence.

Jeshina Janardhanan Ndiif Sem Imaging Award Jeshina Janardhanan

The compound presented in this paper exhibits potent antibacterial activity against C. difficile without significant activity against other major gut bacteria. The compound was shown to target peptidoglycan biosynthesis and through SEM imaging done at NDIIF, we were able to show increasing damage to the cell wall at increasing concentrations of the compound. This is a very significant and worthy image because similar effects of compounds on C. difficile have never been shown before.






Enhanced Li+ Conduction within Single-Ion Conducting Polymer Gel Electrolytes via Reduced Cation–Polymer Interaction

Hunter O. Ford, Bumjun Park, Jizhou Jiang, Morgan E. Seidler, and Jennifer L. Schaefer

ACS Materials Letters. 2020 2, 272-279

An active area of research in the "beyond Li-ion" battery field is the development of new electrolytes. An especially interesting aspect of this field is the development of polymer electrolytes (PEs), where the organic solvent component of conventional electrolytes is replaced with an ion-conducting polymer. In this work, a promising PE is demonstrated that has enhanced Li+ conduction compared to conventional PEs. To understand the PE, and the mechanism of enhance Li+ transport, the polymer was studied with scanning electron microscopy (SEM). It was found that the surface and cross section of the SIPE was dense and homogenous, indicating the enhanced transport comes from something other than morphology. Investigating this material with SEM was non-trivial. The rubbery polymer had to be soaked in liquid N2 to make the polymer glassy, so it could be broken to expose a very clean well-defined cross section. Further, this polymer does not conduct electrons, which leads to charging and poor image quality. The SIPE had to be sputter coated with iridium to allow for high-quality imaging. The results of the SEM allowed us to rule out morphological effects on ion transport, helping us describe the true mechanism and therefore guide future materials engineering efforts.

Hunterford Enhanced Li Figure