New user configurations on the Harmony and Aivia analysis workstation
To help with storage issues, the user configurations on the Harmony and Aivia analysis workstation have changed. You will continue to log in with your identikey and password, but your storage space on the C: Drive (Desktop, Downloads, Documents, etc.) is limited to 5 GB. Your storage space on the D: User Data Drive will be unlimited. Please save all your data to the D: User Data Drive, and please be conscientious of your colleagues.
If you need to download a program or something else that would normally download to C:\Program Files, please contact us and we will add it for you and all other users (to avoid duplicates taking up space on the C: Drive).
We have also added functionality for fast large-data transfer through Globus and access to the CU Boulder Petabyte library and other CU Boulder Research Computing resources.
Nikon Widefield updates
Thank you all for your patience with our Nikon widefield microscope updates. Since November we have added:
- Hamamatsu Orca Fusion: a faster, less noisy camera for fluorescence images with greater contrast between your samples and the background
- Nikon Ti2 base and accessories: a faster internal computer that will be supported by Nikon for years to come
- Windows 11 and NIS Elements upgrade: software that will be supported by Microsoft and by Nikon for years to come
- Sample Overview in NIS Elements: ability to quickly scan your sample at low magnification and set ROIs for imaging at higher magnification
An explanation of changes to the hardware and the software can be found on the Nikon Widefield Wiki.
Opera Phenix automation
The Opera Phenix automation is now running and fully functional! The automation system uses a robot arm to move plates from a fixed-plate rack (max 14 plates) or from a live-cell incubator (max 44 plates) to the Opera Phenix for imaging with plate-specific imaging settings before placing the plate into its original position.
We have developed automation pipelines for the following cases:
- The same imaging settings for one or more plates from the fixed-plate rack or the live-cell incubator
- Different imaging settings for two or more plates from the fixed-plate rack or the live-cell incubator
- The same imaging settings for two or more plates from the live-cell incubator over a timecourse experiment
- Different imaging settings for two or more plates from the live-cell incubator over a timecourse experiment
Please, contact Erin Richards if you are interested in being trained on the automation software.
Recent publications
If you have published recently, please let us know.
- Hannah E Ledvina, Ryan Sayegh, Ricardo O Carale, A Maxwell Burroughs, Alexa R Macklin, Ashely L Azadeh, Layla D Borja Najera, L Aravind, Aaron T Whiteley. Functional amyloid proteins confer defence against predatory bacteria. Nature 644, 197-204 (2025). Microscope(s): Nikon AXR Laser Scanning Confocal.
- Nicole B Day, Christopher R Orear, Alysha N Hunter, Matthew M C Kwan, Christine M Hamadani, Ava d'Auvergne, Junling Guo, Eden E L Tanner, C Wyatt Shields IV. Ionic Liquid-Mediated Delivery of Ruxolitinib to Skin Using an Adhesive Topical Hydrogel System. Adv. Healthcare Mater. 14 (27): e01838 (2025). Microscope(s): Nikon Widefield.
- Anthony Khong, Nina Ripin, Luisa Macedo de Vasconcelos, Victor Passanisi, Sabrina Spencer, Roy Parker. Stress granules promote quiescence by enhancing p21 levels and reducing phospho-Rb. RNA: rna.080635.125 (2025). Microscope(s): Opera Phenix.
- Kelsey Dahlgren, Christopher C Ebmeier, Emily Koke, Jeffrey C Cameron. Spatial proteomics reveals signal sequence characteristics correlated with localization in cyanobacteria. Plant Physiology 198 (4) (2025). Analysis Help: Jian Wei Tay.
- Matthew M C Kwan, Nicole B Day, Iain R Konigsberg, Evan Thoresen, Abigail G Harrell, Celeste E Busch, Elizabeth J Davidson, Ivana V Yang, C Wyatt Shields IV. Particle Shape Modulates the Function of Adoptive Macrophage Transfers. Adv. Healthcare Mater. 14 (31): e01348 (2025). Microscope(s): Nikon Spinning Disk Confocal.
- Nathaniel P Skillin, Lorin Danielsen, Bruce E Kirkpatrick, Jonathan D Hoang, Lea Pearl Hibbard, Kristi S Anseth, Timothy J White. Anisotropic Liquid Crystalline Hydrogels Direct 2D and 3D Myoblast Alignment. Adv. Healthcare Mater. 36 (4): e18226 (2026). Microscope(s): Nikon Spinning Disk Confocal.
- Megan Palacio, Dylan J Taatjes. Real-time visualization of reconstituted transcription reveals RNAPII activation mechanisms at single promoters. Cell Reports 44 (9):116251 (2025). Microscope(s): Nikon N-STORM.
- Aleksandra J Wierzba, Erin M Richards, Shelby R Lennon, Robert T Batey, Amy E Palmer. Enhancement of RNA Imaging Platforms by the Use of Peptide Nucleic Acid-Based Linkers. Bio-protocol 16 (9): e5453 (2025). Microscope(s): Nikon A1R Laser Scanning Confocal.
- Li Yi Cheng, Nina Ripin, Thomas R Cech, Roy Parker. DHX36 modulates stress granule assembly independent of recruitment of mRNAs with G-quadruplex sequence motifs. Nucleic Acids Research 53 (18) (2025). Microscopy Help: Joseph Dragavon.
- Ashley E Sullivan, Ali Nabhani, Daniel S Izrailevsky, Kate Schinkel, Charlotte R K Hoffman, Laurel K Robbins, Toni A Nagy, Melissa L Duncan, Hannah E Ledvina, Annette H Erbse, Emily M Kibby, Uday Tak, David M Dinh, Eirene Marie Q Ednacot, Christy M Nguyen, A Maxwell Burroughs, L Aravind, Aaron T Whiteley, Benjamin R Morehouse. The Panoptes system uses decoy cyclic nucleotides to defend against phage. Nature 647, 988-996 (2025). Microscope(s): Nikon A1R Laser Scanning Confocal.
- Shane D Curry, Talaial B Alina, Sven A Saemundsson, Mariana Cepeda Rodríguez, Bryce M Bower, Jennifer N Cha, Andrew P Goodwin. Effect of Inertial Cavitation by Ultrasound Active Silica Nanoparticles on 2- and 3D Cellular Systems. ACS Applied Nano Mat. 8 (42) (2025). Microscope(s): Nikon AXR Laser Scanning Confocal, Nikon Widefield.
- Alysse DeFoe, Joshua Toth, Abhishek P Dhand, Lovie Deloney, Mackenzie Obenreder, Vivek B Shenoy, Jason A Burdick. Digital light processing of hydrogel molds to guide cell mechanosensing and the fabrication of meniscal tissue constructs. APL Bioeng. 9, 046111 (2025). Microscopy Help: Joseph Dragavon.
- Keisuke Nakamura, Nikolas Di Caprio, Jonathan T Taasan, Cody O Crosby, Jason A Burdick. Dynamic Regulation of Granular Hydrogels Through Guest-Host Interactions to Spatiotemporally Guide Cellular Migration. Adv. Science 13 (5): e12971 (2026). Analysis Workstation(s): Imaris.
- Holly J Coleman, Amber Rauch, Erika Langsfeld, Kimberly Anderson, Urvi Parlikar, Hans H Funke, Robert L Garcea, Theodore W Randolph. Lipid-free, thermostable mRNA vaccines prepared using atomic layer deposition. J. Pharm. Sciences 115 (2), 104066 (2026). Microscope(s): Nikon AXR Laser Scanning Confocal.
- Talaial B Alina, Shane D Curry, Sven A Saemundsson, Bryce M Bower, Jennifer N Cha, Andrew P Goodwin. Focused ultrasound propulsion of acoustically active nanoparticles into gelatin hydrogels. J. Mater. Chem. B 13, 15389-15396 (2025). Microscope(s) and Assistance: Nikon A1R Laser Scanning Confocal and Jian Wei Tay.
- Hannah K Weppner, Maya A Singh, Elizabeth N Katsnelson, David J Douin, Martin D McCarter, Richard P Tobin, Laurel E Hind. Human M-MDSCs impair neutrophil migration in the infectious microenvironment. J. Leukocyte Biol 117 (12): qiaf165 (2025). Microscope(s): Nikon A1R Laser Scanning Confocal.
- Chance C Sine, Lotte P Watts, Brianna Fernandez, Nasreen Marikar, Jianxin Wang, Erik S Knudsen, Agnieszka K Witkiewicz, Sabrina L Spencer. p16 expression confers sensitivity to CDK2 inhibitors in cyclin E1–driven ovarian cancers. Science Signaling 18 (914) (2025). Microscope(s): Opera Phenix.
- Jayson B Ball, Maggie R Finch, Jeremy A Taylor, Zachariah Z Smith, Igor Rafael Correia Rocha, Suzanne M Green-Fulgham, Ethan B Rowe, Joseph M Dragavon, Connor J McNulty, Renee A Dreher, Imaad I Siddique, Gavin Davis, Andrew M Tan, Michael V Baratta, Daniel S Barth, Linda R Watkins. Caudal Granular Insular Cortex to Somatosensory Cortex I: A Critical Pathway for the Transition of Acute to Chronic Pain. J Neurosci 46 (5) (2026). Microscope(s): Nikon A1R Laser Scanning Confocal, Nikon AXR Laser Scanning Confocal, Imaris Analysis Workstation.
- Brianna Fernandez, Victor J Passanisi, Humza M Ashraf, Sabrina L Spencer. Single-cell RNA sequencing reveals a quiescence-senescence continuum and distinct senotypes following chemotherapy. Nature Comm 17 (169) (2026). Microscope(s): Opera Phenix.
- Thomas G Martin, Dakota R Hunt, Christopher C Ebmeier, Abhishek P Dhand, Christina Alamana, Joseph C Cleveland Jr, Sharon L Graw, Sarah Bruner, Michael R Bristow, Luisa Mestroni, Matthew R G Taylor, Jason A Burdick, Amrut V Ambardekar, Peter M Buttrick, Leslie A Leinwand. Myocardial Recovery With Mechanical Circulatory Support Is Linked to Alternative Splicing and Subcellular Localization of CAMK2D. Circulation 153 (9). Microscope(s): Nikon Spinning Disk Confocal.
- Benjamin Nebenfuehr, Lynn Sanford, Erin R Taylor, Kerri Ball, Catherine E Woods-Killam, Hannah I Ghasemi, Bruce Proctor, III, Raquel Ortega, Colin Sempeck, Robin D Dowell, Nausica Arnoult. Uncovering genetic interactions in the DNA repair network in response to endogenous damage and ionizing radiation. Cell Reports 45 (1), 116850 (2026). Microscope(s): Nikon Widefield.
- Morgan B Riffe, Nikolas Di Caprio, Matthew D Davidson, Jason A Burdick. Injectable Bi-layered Cryogel Scaffolds for Targeted Adhesion to Tissues. ACS Macro Letters 15 (2) (2026). Analysis Workstation(s): Imaris.
- Victor Passanisi, Sabrina L Spencer. Replicative senescence induction in single cells is not predicted by telomere length, dysfunction, or oxidation. iScience 29 (3), 114801 (2026). Microscope(s): Nikon AXR Laser Scanning Confocal.
- Eliza S Lee, Ella R Tommer, Paul B Rothman, Sarah V Middleton, Daniel T Youmans, Thomas R Cech. Single-molecule tracking of DNMT1 in living cells reveals its cell cycle dynamics and its redistribution upon drug treatment. Nucleic Acids Research 54 (4) (2026). Microscope(s): Nikon N-STORM.
- Erin R Taylor, Bruce Proctor, III, Melina Vaurs, Guanhui Wu, Manon Mahieu, Shreya Shrestha, Daniel Morrison, Laila Weatherly, Shane Brelinsky, Maya Raghunandan, Anabelle Decottignies, Nausica Arnoult. Local heterochromatin enrichment promotes telomere clustering and PML nuclear body assembly at telomeres. Cell Reports 45 (3), 117004 (2026). Microscope(s): Nikon Spinning Disk Confocal.
- Daniela Trindade, Nikolas Di Caprio, Ana C Maurício, Nuno Alves, Carla Moura, Jason A Burdick. Bioactive and Injectable Granular Hydrogels Incorporating Decellularized Extracellular Matrix. ACS Biomater. Sci. Eng. 12 (3), 1787-1798 (2026). Analysis workstation(s): Imaris.