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1. Responses of pyramidal cell somata and apical dendrites in mouse visual cortex over multiple days

Author

Gillon, Colleen J., Lecoq, Jérôme A., Pina, Jason E., Ahmed, Ruweida, Billeh, Yazan N., Caldejon, Shiella, Groblewski, Peter, Henley, Timothy M., Kato, India, Lee, Eric, Luviano, Jennifer, Mace, Kyla, Nayan, Chelsea, Nguyen, Thuyanh V., North, Kat, Perkins, Jed, Seid, Sam, Valley, Matthew T., Williford, Ali, Bengio, Yoshua, Lillicrap, Timothy P., Zylberberg, Joel, and Richards, Blake A.

Published
2023
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2. Survey of spiking in the mouse visual system reveals functional hierarchy

Author

Siegle, Joshua H., Jia, Xiaoxuan, Durand, Séverine, Gale, Sam, Bennett, Corbett, Graddis, Nile, Heller, Greggory, Ramirez, Tamina K., Choi, Hannah, Luviano, Jennifer A., Groblewski, Peter A., Ahmed, Ruweida, Arkhipov, Anton, Bernard, Amy, Billeh, Yazan N., Brown, Dillan, Buice, Michael A., Cain, Nicolas, Caldejon, Shiella, Casal, Linzy, Cho, Andrew, Chvilicek, Maggie, Cox, Timothy C., Dai, Kael, Denman, Daniel J., de Vries, Saskia E. J., Dietzman, Roald, Esposito, Luke, Farrell, Colin, Feng, David, Galbraith, John, Garrett, Marina, Gelfand, Emily C., Hancock, Nicole, Harris, Julie A., Howard, Robert, Hu, Brian, Hytnen, Ross, Iyer, Ramakrishnan, Jessett, Erika, Johnson, Katelyn, Kato, India, Kiggins, Justin, Lambert, Sophie, Lecoq, Jerome, Ledochowitsch, Peter, Lee, Jung Hoon, Leon, Arielle, Li, Yang, Liang, Elizabeth, Long, Fuhui, Mace, Kyla, Melchior, Jose, Millman, Daniel, Mollenkopf, Tyler, Nayan, Chelsea, Ng, Lydia, Ngo, Kiet, Nguyen, Thuyahn, Nicovich, Philip R., North, Kat, Ocker, Gabriel Koch, Ollerenshaw, Doug, Oliver, Michael, Pachitariu, Marius, Perkins, Jed, Reding, Melissa, Reid, David, Robertson, Miranda, Ronellenfitch, Kara, Seid, Sam, Slaughterbeck, Cliff, Stoecklin, Michelle, Sullivan, David, Sutton, Ben, Swapp, Jackie, Thompson, Carol, Turner, Kristen, Wakeman, Wayne, Whitesell, Jennifer D., Williams, Derric, Williford, Ali, Young, Rob, Zeng, Hongkui, Naylor, Sarah, Phillips, John W., Reid, R. Clay, Mihalas, Stefan, Olsen, Shawn R., and Koch, Christof

Published
2021
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3. Responses to pattern-violating visual stimuli evolve differently over days in somata and distal apical dendrites

Author

Gillon, Colleen J., primary, Pina, Jason E., additional, Lecoq, Jérôme, additional, Ahmed, Ruweida, additional, Billeh, Yazan N., additional, Caldejon, Shiella, additional, Groblewski, Peter A., additional, Henley, Timothy M., additional, Kato, India, additional, Lee, Eric, additional, Luviano, Jennifer, additional, Mace, Kyla, additional, Nayan, Chelsea, additional, Nguyen, Thuyanh V., additional, North, Kat, additional, Perkins, Jed, additional, Seid, Sam, additional, Valley, Matthew T., additional, Williford, Ali, additional, Bengio, Yoshua, additional, Lillicrap, Timothy P., additional, Richards, Blake A., additional, and Zylberberg, Joel, additional

Published
2023
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4. Differential encoding of temporal context and expectation under representational drift across hierarchically connected areas

Author

Wyrick, David G, primary, Cain, Nicholas, additional, Larsen, Rylan S., additional, Lecoq, Jérôme, additional, Valley, Matthew, additional, Ahmed, Ruweida, additional, Bowlus, Jessica, additional, Boyer, Gabriella, additional, Caldejon, Shiella, additional, Casal, Linzy, additional, Chvilicek, Maggie, additional, DePartee, Maxwell, additional, Groblewski, Peter A, additional, Huang, Cindy, additional, Johnson, Katelyn, additional, Kato, India, additional, Larkin, Josh, additional, Lee, Eric, additional, Liang, Elizabeth, additional, Luviano, Jennifer, additional, Mace, Kyla, additional, Nayan, Chelsea, additional, Nguyen, Thuyanhn, additional, Reding, Melissa, additional, Seid, Sam, additional, Sevigny, Joshua, additional, Stoecklin, Michelle, additional, Williford, Ali, additional, Choi, Hannah, additional, Garrett, Marina, additional, and Mazzucato, Luca, additional

Published
2023
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5. Responses to Pattern-Violating Visual Stimuli Evolve Differently Over Days in Somata and Distal Apical Dendrites.

Author

Gillon, Colleen J., Pina, Jason E., Lecoq, Jérôme A., Ahmed, Ruweida, Billeh, Yazan N., Caldejon, Shiella, Groblewski, Peter, Henley, Timothy M., Kato, India, Lee, Eric, Luviano, Jennifer, Mace, Kyla, Nayan, Chelsea, Nguyen, Thuyanh V., North, Kat, Perkins, Jed, Seid, Sam, Valley, Matthew T., Williford, Ali, and Bengio, Yoshua

Subjects
VISUAL perception, PYRAMIDAL neurons, VISUAL cortex, NEOCORTEX, NEURONS
Abstract

Scientists have long conjectured that the neocortex learns patterns in sensory data to generate top-down predictions of upcoming stimuli. In line with this conjecture, different responses to pattern-matching vs pattern-violating visual stimuli have been observed in both spiking and somatic calcium imaging data. However, it remains unknown whether these pattern-violation signals are different between the distal apical dendrites, which are heavily targeted by top-down signals, and the somata, where bottom-up information is primarily integrated. Furthermore, it is unknown how responses to pattern-violating stimuli evolve over time as an animal gains more experience with them. Here, we address these unanswered questions by analyzing responses of individual somata and dendritic branches of layer 2/3 and layer 5 pyramidal neurons tracked over multiple days in primary visual cortex of awake, behaving female and male mice. We use sequences of Gabor patches with patterns in their orientations to create pattern-matching and pattern-violating stimuli, and two-photon calcium imaging to record neuronal responses. Many neurons in both layers show large differences between their responses to pattern-matching and pattern-violating stimuli. Interestingly, these responses evolve in opposite directions in the somata and distal apical dendrites, with somata becoming less sensitive to pattern-violating stimuli and distal apical dendrites more sensitive. These differences between the somata and distal apical dendrites may be important for hierarchical computation of sensory predictions and learning, since these two compartments tend to receive bottom-up and top-down information, respectively. [ABSTRACT FROM AUTHOR]

Published
2024
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6. Stimulus novelty uncovers coding diversity in visual cortical circuits

Author

Garrett, Marina, primary, Groblewski, Peter, additional, Piet, Alex, additional, Ollerenshaw, Doug, additional, Najafi, Farzaneh, additional, Yavorska, Iryna, additional, Amster, Adam, additional, Bennett, Corbett, additional, Buice, Michael, additional, Caldejon, Shiella, additional, Casal, Linzy, additional, D’Orazi, Florence, additional, Daniel, Scott, additional, de Vries, Saskia EJ, additional, Kapner, Daniel, additional, Kiggins, Justin, additional, Lecoq, Jerome, additional, Ledochowitsch, Peter, additional, Manavi, Sahar, additional, Mei, Nicholas, additional, Morrison, Christopher B., additional, Naylor, Sarah, additional, Orlova, Natalia, additional, Perkins, Jed, additional, Ponvert, Nick, additional, Roll, Clark, additional, Seid, Sam, additional, Williams, Derric, additional, Williford, Allison, additional, Ahmed, Ruweida, additional, Amine, Daniel, additional, Billeh, Yazan, additional, Bowman, Chris, additional, Cain, Nicholas, additional, Cho, Andrew, additional, Dawe, Tim, additional, Departee, Max, additional, Desoto, Marie, additional, Feng, David, additional, Gale, Sam, additional, Gelfand, Emily, additional, Gradis, Nile, additional, Grasso, Conor, additional, Hancock, Nicole, additional, Hu, Brian, additional, Hytnen, Ross, additional, Jia, Xiaoxuan, additional, Johnson, Tye, additional, Kato, India, additional, Kivikas, Sara, additional, Kuan, Leonard, additional, L’Heureux, Quinn, additional, Lambert, Sophie, additional, Leon, Arielle, additional, Liang, Elizabeth, additional, Long, Fuhui, additional, Mace, Kyla, additional, Magrans de Abril, Ildefons, additional, Mochizuki, Chris, additional, Nayan, Chelsea, additional, North, Katherine, additional, Ng, Lydia, additional, Ocker, Gabriel Koch, additional, Oliver, Michael, additional, Rhoads, Paul, additional, Ronellenfitch, Kara, additional, Schelonka, Kathryn, additional, Sevigny, Josh, additional, Sullivan, David, additional, Sutton, Ben, additional, Swapp, Jackie, additional, Nguyen, Thuyanh K, additional, Waughman, Xana, additional, Wilkes, Joshua, additional, Wang, Michael, additional, Farrell, Colin, additional, Wakeman, Wayne, additional, Zeng, Hongkui, additional, Phillips, John, additional, Mihalas, Stefan, additional, Arkhipov, Anton, additional, Koch, Christof, additional, and Olsen, Shawn R, additional

Published
2023
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7. A Standardized Nonvisual Behavioral Event Is Broadcasted Homogeneously across Cortical Visual Areas without Modulating Visual Responses

Author

Ramadan, Mahdi, primary, Lee, Eric Kenji, additional, de Vries, Saskia, additional, Caldejon, Shiella, additional, Kato, India, additional, Roll, Kate, additional, Griffin, Fiona, additional, Nguyen, Thuyanh V., additional, Larkin, Josh, additional, Rhoads, Paul, additional, Mace, Kyla, additional, Kriedberg, Ali, additional, Howard, Robert, additional, Berbesque, Nathan, additional, and Lecoq, Jérôme, additional

Published
2022
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8. Reconciling functional differences in populations of neurons recorded with two-photon imaging and electrophysiology

Author

Siegle, Joshua H, primary, Ledochowitsch, Peter, additional, Jia, Xiaoxuan, additional, Millman, Daniel J, additional, Ocker, Gabriel K, additional, Caldejon, Shiella, additional, Casal, Linzy, additional, Cho, Andy, additional, Denman, Daniel J, additional, Durand, Séverine, additional, Groblewski, Peter A, additional, Heller, Gregg, additional, Kato, India, additional, Kivikas, Sara, additional, Lecoq, Jérôme, additional, Nayan, Chelsea, additional, Ngo, Kiet, additional, Nicovich, Philip R, additional, North, Kat, additional, Ramirez, Tamina K, additional, Swapp, Jackie, additional, Waughman, Xana, additional, Williford, Ali, additional, Olsen, Shawn R, additional, Koch, Christof, additional, Buice, Michael A, additional, and de Vries, Saskia EJ, additional

Published
2021
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9. Author response: Reconciling functional differences in populations of neurons recorded with two-photon imaging and electrophysiology

Author

Siegle, Joshua H, primary, Ledochowitsch, Peter, additional, Jia, Xiaoxuan, additional, Millman, Daniel J, additional, Ocker, Gabriel K, additional, Caldejon, Shiella, additional, Casal, Linzy, additional, Cho, Andy, additional, Denman, Daniel J, additional, Durand, Séverine, additional, Groblewski, Peter A, additional, Heller, Gregg, additional, Kato, India, additional, Kivikas, Sara, additional, Lecoq, Jérôme, additional, Nayan, Chelsea, additional, Ngo, Kiet, additional, Nicovich, Philip R, additional, North, Kat, additional, Ramirez, Tamina K, additional, Swapp, Jackie, additional, Waughman, Xana, additional, Williford, Ali, additional, Olsen, Shawn R, additional, Koch, Christof, additional, Buice, Michael A, additional, and de Vries, Saskia EJ, additional

Published
2021
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10. Learning from unexpected events in the neocortical microcircuit

Author

Gillon, Colleen J., primary, Pina, Jason E., additional, Lecoq, Jérôme A., additional, Ahmed, Ruweida, additional, Billeh, Yazan N., additional, Caldejon, Shiella, additional, Groblewski, Peter, additional, Henley, Timothy M., additional, Kato, India, additional, Lee, Eric, additional, Luviano, Jennifer, additional, Mace, Kyla, additional, Nayan, Chelsea, additional, Nguyen, Thuyanh V., additional, North, Kat, additional, Perkins, Jed, additional, Seid, Sam, additional, Valley, Matthew T., additional, Williford, Ali, additional, Bengio, Yoshua, additional, Lillicrap, Timothy P., additional, Richards, Blake A., additional, and Zylberberg, Joel, additional

Published
2021
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11. A standardized behavioral event equally impacts the activity of cortical visual areas and layers

Author

Ramadan, Mahdi, primary, Lee, Eric Kenji, additional, Caldejon, Shiella, additional, Kato, India, additional, Roll, Kate, additional, Griffin, Fiona, additional, Nguyen, Thuyanh V., additional, Larkin, Josh, additional, Rhoads, Paul, additional, Mace, Kyla, additional, Kriedberg, Ali, additional, Howard, Robert, additional, Berbesque, Nathan, additional, and Lecoq, Jérôme, additional

Published
2020
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12. VIP interneurons in mouse primary visual cortex selectively enhance responses to weak but specific stimuli

Author

Millman, Daniel J, primary, Ocker, Gabriel Koch, additional, Caldejon, Shiella, additional, Kato, India, additional, Larkin, Josh D, additional, Lee, Eric Kenji, additional, Luviano, Jennifer, additional, Nayan, Chelsea, additional, Nguyen, Thuyanh V, additional, North, Kat, additional, Seid, Sam, additional, White, Cassandra, additional, Lecoq, Jerome, additional, Reid, Clay, additional, Buice, Michael A, additional, and de Vries, Saskia EJ, additional

Published
2020
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13. Multiplane Mesoscope reveals distinct cortical interactions following expectation violations

Author

Orlova, Natalia, primary, Najafi, Farzaneh, additional, Tsyboulski, Dmitri, additional, Seid, Sam, additional, Kivikas, Sara, additional, Kato, India, additional, Griffin, Fiona, additional, Leon, Arielle, additional, Hytnen, Ross D., additional, L’Heureux, Quinn, additional, North, Kat, additional, Swapp, Jackie, additional, Nayan, Chelsea, additional, Hancock, Nicole, additional, Ahmed, Ruweida, additional, Gelfand, Emily, additional, Cho, Andrew, additional, Mace, Kyla, additional, Howard, Robert, additional, Casal, Linzy, additional, Lambert, Sophie, additional, Lee, Eric Kenji, additional, Caldejon, Shiella, additional, Waughman, Xana, additional, Williford, Allison, additional, Garrett, Marina, additional, Ollerenshaw, Doug, additional, Olsen, Shawn R., additional, Groblewski, Peter A., additional, Saggau, Peter, additional, and Lecoq, Jérôme, additional

Published
2020
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14. Author response: VIP interneurons in mouse primary visual cortex selectively enhance responses to weak but specific stimuli

Author

Millman, Daniel J, primary, Ocker, Gabriel Koch, additional, Caldejon, Shiella, additional, Kato, India, additional, Larkin, Josh D, additional, Lee, Eric Kenji, additional, Luviano, Jennifer, additional, Nayan, Chelsea, additional, Nguyen, Thuyanh V, additional, North, Kat, additional, Seid, Sam, additional, White, Cassandra, additional, Lecoq, Jerome, additional, Reid, Clay, additional, Buice, Michael A, additional, and de Vries, Saskia EJ, additional

Published
2020
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15. Reconciling functional differences in populations of neurons recorded with two-photon imaging and electrophysiology

Author

Siegle, Joshua H., primary, Ledochowitsch, Peter, additional, Jia, Xiaoxuan, additional, Millman, Daniel, additional, Ocker, Gabriel K., additional, Caldejon, Shiella, additional, Casal, Linzy, additional, Cho, Andrew, additional, Denman, Daniel J., additional, Durand, Séverine, additional, Groblewski, Peter A., additional, Heller, Greggory, additional, Kato, India, additional, Kivikas, Sara, additional, Lecoq, Jerome, additional, Nayan, Chelsea, additional, Ngo, Kiet, additional, Nicovich, Philip R., additional, North, Kat R., additional, Ramirez, Tamina K., additional, Swapp, Jackie, additional, Waughman, Xana, additional, Williford, Ali, additional, Olsen, Shawn R., additional, Koch, Christof, additional, Buice, Michael A., additional, and de Vries, Saskia E. J., additional

Published
2020
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16. VIP interneurons selectively enhance weak but behaviorally-relevant stimuli

Author

Millman, Daniel J., primary, Ocker, Gabriel Koch, additional, Caldejon, Shiella, additional, Kato, India, additional, Larkin, Josh D., additional, Lee, Eric Kenji, additional, Luviano, Jennifer, additional, Nayan, Chelsea, additional, Nguyen, Thuyanh V., additional, North, Kat, additional, Seid, Sam, additional, White, Cassandra, additional, Lecoq, Jerome A., additional, Reid, R. Clay, additional, Buice, Michael A., additional, and de Vries, Saskia E.J., additional

Published
2019
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17. A survey of spiking activity reveals a functional hierarchy of mouse corticothalamic visual areas

Author

Siegle, Joshua H., primary, Jia, Xiaoxuan, additional, Durand, Séverine, additional, Gale, Sam, additional, Bennett, Corbett, additional, Graddis, Nile, additional, Heller, Greggory, additional, Ramirez, Tamina K., additional, Choi, Hannah, additional, Luviano, Jennifer A., additional, Groblewski, Peter A., additional, Ahmed, Ruweida, additional, Arkhipov, Anton, additional, Bernard, Amy, additional, Billeh, Yazan N., additional, Brown, Dillan, additional, Buice, Michael A., additional, Cain, Nicolas, additional, Caldejon, Shiella, additional, Casal, Linzy, additional, Cho, Andrew, additional, Chvilicek, Maggie, additional, Cox, Timothy C., additional, Dai, Kael, additional, Denman, Daniel J., additional, de Vries, Saskia E. J., additional, Dietzman, Roald, additional, Esposito, Luke, additional, Farrell, Colin, additional, Feng, David, additional, Galbraith, John, additional, Garrett, Marina, additional, Gelfand, Emily C., additional, Hancock, Nicole, additional, Harris, Julie A., additional, Howard, Robert, additional, Hu, Brian, additional, Hytnen, Ross, additional, Iyer, Ramakrishnan, additional, Jessett, Erika, additional, Johnson, Katelyn, additional, Kato, India, additional, Kiggins, Justin, additional, Lambert, Sophie, additional, Lecoq, Jerome, additional, Ledochowitsch, Peter, additional, Lee, Jung Hoon, additional, Leon, Arielle, additional, Li, Yang, additional, Liang, Elizabeth, additional, Long, Fuhui, additional, Mace, Kyla, additional, Melchior, Jose, additional, Millman, Daniel, additional, Mollenkopf, Tyler, additional, Nayan, Chelsea, additional, Ng, Lydia, additional, Ngo, Kiet, additional, Nguyen, Thuyahn, additional, Nicovich, Philip R., additional, North, Kat, additional, Ocker, Gabriel Koch, additional, Ollerenshaw, Doug, additional, Oliver, Michael, additional, Pachitariu, Marius, additional, Perkins, Jed, additional, Reding, Melissa, additional, Reid, David, additional, Robertson, Miranda, additional, Ronellenfitch, Kara, additional, Seid, Sam, additional, Slaughterbeck, Cliff, additional, Stoecklin, Michelle, additional, Sullivan, David, additional, Sutton, Ben, additional, Swapp, Jackie, additional, Thompson, Carol, additional, Turner, Kristen, additional, Wakeman, Wayne, additional, Whitesell, Jennifer D., additional, Williams, Derric, additional, Williford, Ali, additional, Young, Rob, additional, Zeng, Hongkui, additional, Naylor, Sarah, additional, Phillips, John W., additional, Reid, R. Clay, additional, Mihalas, Stefan, additional, Olsen, Shawn R., additional, and Koch, Christof, additional

Published
2019
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19. Differential encoding of temporal context and expectation under representational drift across hierarchically connected areas.

Author

Wyrick DG, Cain N, Larsen RS, Lecoq J, Valley M, Ahmed R, Bowlus J, Boyer G, Caldejon S, Casal L, Chvilicek M, DePartee M, Groblewski PA, Huang C, Johnson K, Kato I, Larkin J, Lee E, Liang E, Luviano J, Mace K, Nayan C, Nguyen T, Reding M, Seid S, Sevigny J, Stoecklin M, Williford A, Choi H, Garrett M, and Mazzucato L

Abstract

The classic view that neural populations in sensory cortices preferentially encode responses to incoming stimuli has been strongly challenged by recent experimental studies. Despite the fact that a large fraction of variance of visual responses in rodents can be attributed to behavioral state and movements, trial-history, and salience, the effects of contextual modulations and expectations on sensory-evoked responses in visual and association areas remain elusive. Here, we present a comprehensive experimental and theoretical study showing that hierarchically connected visual and association areas differentially encode the temporal context and expectation of naturalistic visual stimuli, consistent with the theory of hierarchical predictive coding. We measured neural responses to expected and unexpected sequences of natural scenes in the primary visual cortex (V1), the posterior medial higher order visual area (PM), and retrosplenial cortex (RSP) using 2-photon imaging in behaving mice collected through the Allen Institute Mindscope's OpenScope program. We found that information about image identity in neural population activity depended on the temporal context of transitions preceding each scene, and decreased along the hierarchy. Furthermore, our analyses revealed that the conjunctive encoding of temporal context and image identity was modulated by expectations of sequential events. In V1 and PM, we found enhanced and specific responses to unexpected oddball images, signaling stimulus-specific expectation violation. In contrast, in RSP the population response to oddball presentation recapitulated the missing expected image rather than the oddball image. These differential responses along the hierarchy are consistent with classic theories of hierarchical predictive coding whereby higher areas encode predictions and lower areas encode deviations from expectation. We further found evidence for drift in visual responses on the timescale of minutes. Although activity drift was present in all areas, population responses in V1 and PM, but not in RSP, maintained stable encoding of visual information and representational geometry. Instead we found that RSP drift was independent of stimulus information, suggesting a role in generating an internal model of the environment in the temporal domain. Overall, our results establish temporal context and expectation as substantial encoding dimensions in the visual cortex subject to fast representational drift and suggest that hierarchically connected areas instantiate a predictive coding mechanism., Competing Interests: Declaration of interests The authors declare no competing interests.

Published
2023
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