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end to end cnmf e  (Inscopix Inc)
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In vivo calcium imaging was used to record longitudinal neuronal activity in dorsal CA1 during learning, post-learning NE, and OLM testing. ( A1) . Schematic of the miniscope placement, lens track, and GCaMP7f expression. Scale bar: 100 µm. ( A2) . Generation of the processed footprint from raw image by <t>CNMF-E.</t> ( A3) . Representative cell traces. ( B) . Behavior procedures ( B1 ) along with task-specific calcium imaging ( B2 ) with control mice, mice subjected to NE 0.5 hr post-learning (the 0.5-hr NE group), and mice subjected to NE at 4 hr post-learning (the 4-hr NE group). ( C) . The in vivo calcium imaging procedure does not affect learning [ C1 , F (2,18)=0.4, p=0.6761] and the outcome of OLM [ C2 , F (2,18)=19.20, p <0.0001] [ C3 , F (2,18)=19.20, p<0.0001]. While the control and 4-hr NE group showed normal OLM, the 0.5-hr NE group forgot. ( D) . Mean amplitude during training (all groups), post-training in home cage (control group), post-training NE (0.5-hr and 4-hr NE groups), and testing (all groups) [F (4,36)=1.249, p=0.3080]. ( E) . Mean event rate during training (all groups), post-training in home cage (control group), post-training NE (0.5-hr and 4-hr NE groups), and testing (all groups) [F (4,36)=0.07365, p=0.9897]. ( F1) . Ensemble reactivation during post-learning recording [F (2,18)=2.710, p=0.0936]. ( F2) . Ensemble reactivation during testing [F (2,18)=4.852, p=0.0206]. ( F3) . Spearman and Pearson analysis were used to determine correlation between discrimination ratio and % of the learning-associated ensemble reactivation during testing. ( G1) . % of total neurons uniquely detected during NE. ( G2) . % of reactivation of NE-specific neurons during testing. Data are presented as mean +/-SEM (n=7 for each group). Data were analyzed by unpaired t-test ( G1 and G2 ) and two-way ANOVA ( C1, C2, D , and E ) or one-way-ANOVA ( C3, F1 , and F2 ) followed by post-hoc pairwise comparison.
End To End Cnmf E, supplied by Inscopix Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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non negative matrix factorization cnmf e pipeline  (Inscopix Inc)
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In vivo calcium imaging was used to record longitudinal neuronal activity in dorsal CA1 during learning, post-learning NE, and OLM testing. ( A1) . Schematic of the miniscope placement, lens track, and GCaMP7f expression. Scale bar: 100 µm. ( A2) . Generation of the processed footprint from raw image by <t>CNMF-E.</t> ( A3) . Representative cell traces. ( B) . Behavior procedures ( B1 ) along with task-specific calcium imaging ( B2 ) with control mice, mice subjected to NE 0.5 hr post-learning (the 0.5-hr NE group), and mice subjected to NE at 4 hr post-learning (the 4-hr NE group). ( C) . The in vivo calcium imaging procedure does not affect learning [ C1 , F (2,18)=0.4, p=0.6761] and the outcome of OLM [ C2 , F (2,18)=19.20, p <0.0001] [ C3 , F (2,18)=19.20, p<0.0001]. While the control and 4-hr NE group showed normal OLM, the 0.5-hr NE group forgot. ( D) . Mean amplitude during training (all groups), post-training in home cage (control group), post-training NE (0.5-hr and 4-hr NE groups), and testing (all groups) [F (4,36)=1.249, p=0.3080]. ( E) . Mean event rate during training (all groups), post-training in home cage (control group), post-training NE (0.5-hr and 4-hr NE groups), and testing (all groups) [F (4,36)=0.07365, p=0.9897]. ( F1) . Ensemble reactivation during post-learning recording [F (2,18)=2.710, p=0.0936]. ( F2) . Ensemble reactivation during testing [F (2,18)=4.852, p=0.0206]. ( F3) . Spearman and Pearson analysis were used to determine correlation between discrimination ratio and % of the learning-associated ensemble reactivation during testing. ( G1) . % of total neurons uniquely detected during NE. ( G2) . % of reactivation of NE-specific neurons during testing. Data are presented as mean +/-SEM (n=7 for each group). Data were analyzed by unpaired t-test ( G1 and G2 ) and two-way ANOVA ( C1, C2, D , and E ) or one-way-ANOVA ( C3, F1 , and F2 ) followed by post-hoc pairwise comparison.
Non Negative Matrix Factorization Cnmf E Pipeline, supplied by Inscopix Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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extended constrained non-negative matrix factorization (cnmf-e)  (MathWorks Inc)
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MathWorks Inc extended constrained non-negative matrix factorization (cnmf-e)
In vivo calcium imaging was used to record longitudinal neuronal activity in dorsal CA1 during learning, post-learning NE, and OLM testing. ( A1) . Schematic of the miniscope placement, lens track, and GCaMP7f expression. Scale bar: 100 µm. ( A2) . Generation of the processed footprint from raw image by <t>CNMF-E.</t> ( A3) . Representative cell traces. ( B) . Behavior procedures ( B1 ) along with task-specific calcium imaging ( B2 ) with control mice, mice subjected to NE 0.5 hr post-learning (the 0.5-hr NE group), and mice subjected to NE at 4 hr post-learning (the 4-hr NE group). ( C) . The in vivo calcium imaging procedure does not affect learning [ C1 , F (2,18)=0.4, p=0.6761] and the outcome of OLM [ C2 , F (2,18)=19.20, p <0.0001] [ C3 , F (2,18)=19.20, p<0.0001]. While the control and 4-hr NE group showed normal OLM, the 0.5-hr NE group forgot. ( D) . Mean amplitude during training (all groups), post-training in home cage (control group), post-training NE (0.5-hr and 4-hr NE groups), and testing (all groups) [F (4,36)=1.249, p=0.3080]. ( E) . Mean event rate during training (all groups), post-training in home cage (control group), post-training NE (0.5-hr and 4-hr NE groups), and testing (all groups) [F (4,36)=0.07365, p=0.9897]. ( F1) . Ensemble reactivation during post-learning recording [F (2,18)=2.710, p=0.0936]. ( F2) . Ensemble reactivation during testing [F (2,18)=4.852, p=0.0206]. ( F3) . Spearman and Pearson analysis were used to determine correlation between discrimination ratio and % of the learning-associated ensemble reactivation during testing. ( G1) . % of total neurons uniquely detected during NE. ( G2) . % of reactivation of NE-specific neurons during testing. Data are presented as mean +/-SEM (n=7 for each group). Data were analyzed by unpaired t-test ( G1 and G2 ) and two-way ANOVA ( C1, C2, D , and E ) or one-way-ANOVA ( C3, F1 , and F2 ) followed by post-hoc pairwise comparison.
Extended Constrained Non Negative Matrix Factorization (Cnmf E), supplied by MathWorks Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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In vivo calcium imaging was used to record longitudinal neuronal activity in dorsal CA1 during learning, post-learning NE, and OLM testing. ( A1) . Schematic of the miniscope placement, lens track, and GCaMP7f expression. Scale bar: 100 µm. ( A2) . Generation of the processed footprint from raw image by <t>CNMF-E.</t> ( A3) . Representative cell traces. ( B) . Behavior procedures ( B1 ) along with task-specific calcium imaging ( B2 ) with control mice, mice subjected to NE 0.5 hr post-learning (the 0.5-hr NE group), and mice subjected to NE at 4 hr post-learning (the 4-hr NE group). ( C) . The in vivo calcium imaging procedure does not affect learning [ C1 , F (2,18)=0.4, p=0.6761] and the outcome of OLM [ C2 , F (2,18)=19.20, p <0.0001] [ C3 , F (2,18)=19.20, p<0.0001]. While the control and 4-hr NE group showed normal OLM, the 0.5-hr NE group forgot. ( D) . Mean amplitude during training (all groups), post-training in home cage (control group), post-training NE (0.5-hr and 4-hr NE groups), and testing (all groups) [F (4,36)=1.249, p=0.3080]. ( E) . Mean event rate during training (all groups), post-training in home cage (control group), post-training NE (0.5-hr and 4-hr NE groups), and testing (all groups) [F (4,36)=0.07365, p=0.9897]. ( F1) . Ensemble reactivation during post-learning recording [F (2,18)=2.710, p=0.0936]. ( F2) . Ensemble reactivation during testing [F (2,18)=4.852, p=0.0206]. ( F3) . Spearman and Pearson analysis were used to determine correlation between discrimination ratio and % of the learning-associated ensemble reactivation during testing. ( G1) . % of total neurons uniquely detected during NE. ( G2) . % of reactivation of NE-specific neurons during testing. Data are presented as mean +/-SEM (n=7 for each group). Data were analyzed by unpaired t-test ( G1 and G2 ) and two-way ANOVA ( C1, C2, D , and E ) or one-way-ANOVA ( C3, F1 , and F2 ) followed by post-hoc pairwise comparison.
Cnmf E Pipeline, supplied by Inscopix Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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implementation of cnmf  (MathWorks Inc)
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MathWorks Inc implementation of cnmf
In vivo calcium imaging was used to record longitudinal neuronal activity in dorsal CA1 during learning, post-learning NE, and OLM testing. ( A1) . Schematic of the miniscope placement, lens track, and GCaMP7f expression. Scale bar: 100 µm. ( A2) . Generation of the processed footprint from raw image by <t>CNMF-E.</t> ( A3) . Representative cell traces. ( B) . Behavior procedures ( B1 ) along with task-specific calcium imaging ( B2 ) with control mice, mice subjected to NE 0.5 hr post-learning (the 0.5-hr NE group), and mice subjected to NE at 4 hr post-learning (the 4-hr NE group). ( C) . The in vivo calcium imaging procedure does not affect learning [ C1 , F (2,18)=0.4, p=0.6761] and the outcome of OLM [ C2 , F (2,18)=19.20, p <0.0001] [ C3 , F (2,18)=19.20, p<0.0001]. While the control and 4-hr NE group showed normal OLM, the 0.5-hr NE group forgot. ( D) . Mean amplitude during training (all groups), post-training in home cage (control group), post-training NE (0.5-hr and 4-hr NE groups), and testing (all groups) [F (4,36)=1.249, p=0.3080]. ( E) . Mean event rate during training (all groups), post-training in home cage (control group), post-training NE (0.5-hr and 4-hr NE groups), and testing (all groups) [F (4,36)=0.07365, p=0.9897]. ( F1) . Ensemble reactivation during post-learning recording [F (2,18)=2.710, p=0.0936]. ( F2) . Ensemble reactivation during testing [F (2,18)=4.852, p=0.0206]. ( F3) . Spearman and Pearson analysis were used to determine correlation between discrimination ratio and % of the learning-associated ensemble reactivation during testing. ( G1) . % of total neurons uniquely detected during NE. ( G2) . % of reactivation of NE-specific neurons during testing. Data are presented as mean +/-SEM (n=7 for each group). Data were analyzed by unpaired t-test ( G1 and G2 ) and two-way ANOVA ( C1, C2, D , and E ) or one-way-ANOVA ( C3, F1 , and F2 ) followed by post-hoc pairwise comparison.
Implementation Of Cnmf, supplied by MathWorks Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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code of cnmf-e  (MathWorks Inc)
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In vivo calcium imaging was used to record longitudinal neuronal activity in dorsal CA1 during learning, post-learning NE, and OLM testing. ( A1) . Schematic of the miniscope placement, lens track, and GCaMP7f expression. Scale bar: 100 µm. ( A2) . Generation of the processed footprint from raw image by <t>CNMF-E.</t> ( A3) . Representative cell traces. ( B) . Behavior procedures ( B1 ) along with task-specific calcium imaging ( B2 ) with control mice, mice subjected to NE 0.5 hr post-learning (the 0.5-hr NE group), and mice subjected to NE at 4 hr post-learning (the 4-hr NE group). ( C) . The in vivo calcium imaging procedure does not affect learning [ C1 , F (2,18)=0.4, p=0.6761] and the outcome of OLM [ C2 , F (2,18)=19.20, p <0.0001] [ C3 , F (2,18)=19.20, p<0.0001]. While the control and 4-hr NE group showed normal OLM, the 0.5-hr NE group forgot. ( D) . Mean amplitude during training (all groups), post-training in home cage (control group), post-training NE (0.5-hr and 4-hr NE groups), and testing (all groups) [F (4,36)=1.249, p=0.3080]. ( E) . Mean event rate during training (all groups), post-training in home cage (control group), post-training NE (0.5-hr and 4-hr NE groups), and testing (all groups) [F (4,36)=0.07365, p=0.9897]. ( F1) . Ensemble reactivation during post-learning recording [F (2,18)=2.710, p=0.0936]. ( F2) . Ensemble reactivation during testing [F (2,18)=4.852, p=0.0206]. ( F3) . Spearman and Pearson analysis were used to determine correlation between discrimination ratio and % of the learning-associated ensemble reactivation during testing. ( G1) . % of total neurons uniquely detected during NE. ( G2) . % of reactivation of NE-specific neurons during testing. Data are presented as mean +/-SEM (n=7 for each group). Data were analyzed by unpaired t-test ( G1 and G2 ) and two-way ANOVA ( C1, C2, D , and E ) or one-way-ANOVA ( C3, F1 , and F2 ) followed by post-hoc pairwise comparison.
Code Of Cnmf E, supplied by MathWorks Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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cnmf-e algorithms custom-written matlab codes  (MathWorks Inc)
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In vivo calcium imaging was used to record longitudinal neuronal activity in dorsal CA1 during learning, post-learning NE, and OLM testing. ( A1) . Schematic of the miniscope placement, lens track, and GCaMP7f expression. Scale bar: 100 µm. ( A2) . Generation of the processed footprint from raw image by <t>CNMF-E.</t> ( A3) . Representative cell traces. ( B) . Behavior procedures ( B1 ) along with task-specific calcium imaging ( B2 ) with control mice, mice subjected to NE 0.5 hr post-learning (the 0.5-hr NE group), and mice subjected to NE at 4 hr post-learning (the 4-hr NE group). ( C) . The in vivo calcium imaging procedure does not affect learning [ C1 , F (2,18)=0.4, p=0.6761] and the outcome of OLM [ C2 , F (2,18)=19.20, p <0.0001] [ C3 , F (2,18)=19.20, p<0.0001]. While the control and 4-hr NE group showed normal OLM, the 0.5-hr NE group forgot. ( D) . Mean amplitude during training (all groups), post-training in home cage (control group), post-training NE (0.5-hr and 4-hr NE groups), and testing (all groups) [F (4,36)=1.249, p=0.3080]. ( E) . Mean event rate during training (all groups), post-training in home cage (control group), post-training NE (0.5-hr and 4-hr NE groups), and testing (all groups) [F (4,36)=0.07365, p=0.9897]. ( F1) . Ensemble reactivation during post-learning recording [F (2,18)=2.710, p=0.0936]. ( F2) . Ensemble reactivation during testing [F (2,18)=4.852, p=0.0206]. ( F3) . Spearman and Pearson analysis were used to determine correlation between discrimination ratio and % of the learning-associated ensemble reactivation during testing. ( G1) . % of total neurons uniquely detected during NE. ( G2) . % of reactivation of NE-specific neurons during testing. Data are presented as mean +/-SEM (n=7 for each group). Data were analyzed by unpaired t-test ( G1 and G2 ) and two-way ANOVA ( C1, C2, D , and E ) or one-way-ANOVA ( C3, F1 , and F2 ) followed by post-hoc pairwise comparison.
Cnmf E Algorithms Custom Written Matlab Codes, supplied by MathWorks Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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cnmf-e  (Mendeley Ltd)
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In vivo calcium imaging was used to record longitudinal neuronal activity in dorsal CA1 during learning, post-learning NE, and OLM testing. ( A1) . Schematic of the miniscope placement, lens track, and GCaMP7f expression. Scale bar: 100 µm. ( A2) . Generation of the processed footprint from raw image by <t>CNMF-E.</t> ( A3) . Representative cell traces. ( B) . Behavior procedures ( B1 ) along with task-specific calcium imaging ( B2 ) with control mice, mice subjected to NE 0.5 hr post-learning (the 0.5-hr NE group), and mice subjected to NE at 4 hr post-learning (the 4-hr NE group). ( C) . The in vivo calcium imaging procedure does not affect learning [ C1 , F (2,18)=0.4, p=0.6761] and the outcome of OLM [ C2 , F (2,18)=19.20, p <0.0001] [ C3 , F (2,18)=19.20, p<0.0001]. While the control and 4-hr NE group showed normal OLM, the 0.5-hr NE group forgot. ( D) . Mean amplitude during training (all groups), post-training in home cage (control group), post-training NE (0.5-hr and 4-hr NE groups), and testing (all groups) [F (4,36)=1.249, p=0.3080]. ( E) . Mean event rate during training (all groups), post-training in home cage (control group), post-training NE (0.5-hr and 4-hr NE groups), and testing (all groups) [F (4,36)=0.07365, p=0.9897]. ( F1) . Ensemble reactivation during post-learning recording [F (2,18)=2.710, p=0.0936]. ( F2) . Ensemble reactivation during testing [F (2,18)=4.852, p=0.0206]. ( F3) . Spearman and Pearson analysis were used to determine correlation between discrimination ratio and % of the learning-associated ensemble reactivation during testing. ( G1) . % of total neurons uniquely detected during NE. ( G2) . % of reactivation of NE-specific neurons during testing. Data are presented as mean +/-SEM (n=7 for each group). Data were analyzed by unpaired t-test ( G1 and G2 ) and two-way ANOVA ( C1, C2, D , and E ) or one-way-ANOVA ( C3, F1 , and F2 ) followed by post-hoc pairwise comparison.
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Image Search Results


In vivo calcium imaging was used to record longitudinal neuronal activity in dorsal CA1 during learning, post-learning NE, and OLM testing. ( A1) . Schematic of the miniscope placement, lens track, and GCaMP7f expression. Scale bar: 100 µm. ( A2) . Generation of the processed footprint from raw image by CNMF-E. ( A3) . Representative cell traces. ( B) . Behavior procedures ( B1 ) along with task-specific calcium imaging ( B2 ) with control mice, mice subjected to NE 0.5 hr post-learning (the 0.5-hr NE group), and mice subjected to NE at 4 hr post-learning (the 4-hr NE group). ( C) . The in vivo calcium imaging procedure does not affect learning [ C1 , F (2,18)=0.4, p=0.6761] and the outcome of OLM [ C2 , F (2,18)=19.20, p <0.0001] [ C3 , F (2,18)=19.20, p<0.0001]. While the control and 4-hr NE group showed normal OLM, the 0.5-hr NE group forgot. ( D) . Mean amplitude during training (all groups), post-training in home cage (control group), post-training NE (0.5-hr and 4-hr NE groups), and testing (all groups) [F (4,36)=1.249, p=0.3080]. ( E) . Mean event rate during training (all groups), post-training in home cage (control group), post-training NE (0.5-hr and 4-hr NE groups), and testing (all groups) [F (4,36)=0.07365, p=0.9897]. ( F1) . Ensemble reactivation during post-learning recording [F (2,18)=2.710, p=0.0936]. ( F2) . Ensemble reactivation during testing [F (2,18)=4.852, p=0.0206]. ( F3) . Spearman and Pearson analysis were used to determine correlation between discrimination ratio and % of the learning-associated ensemble reactivation during testing. ( G1) . % of total neurons uniquely detected during NE. ( G2) . % of reactivation of NE-specific neurons during testing. Data are presented as mean +/-SEM (n=7 for each group). Data were analyzed by unpaired t-test ( G1 and G2 ) and two-way ANOVA ( C1, C2, D , and E ) or one-way-ANOVA ( C3, F1 , and F2 ) followed by post-hoc pairwise comparison.

Journal: bioRxiv

Article Title: Contamination of Engram Coactivity Networks During Forgetting

doi: 10.64898/2026.04.21.719933

Figure Lengend Snippet: In vivo calcium imaging was used to record longitudinal neuronal activity in dorsal CA1 during learning, post-learning NE, and OLM testing. ( A1) . Schematic of the miniscope placement, lens track, and GCaMP7f expression. Scale bar: 100 µm. ( A2) . Generation of the processed footprint from raw image by CNMF-E. ( A3) . Representative cell traces. ( B) . Behavior procedures ( B1 ) along with task-specific calcium imaging ( B2 ) with control mice, mice subjected to NE 0.5 hr post-learning (the 0.5-hr NE group), and mice subjected to NE at 4 hr post-learning (the 4-hr NE group). ( C) . The in vivo calcium imaging procedure does not affect learning [ C1 , F (2,18)=0.4, p=0.6761] and the outcome of OLM [ C2 , F (2,18)=19.20, p <0.0001] [ C3 , F (2,18)=19.20, p<0.0001]. While the control and 4-hr NE group showed normal OLM, the 0.5-hr NE group forgot. ( D) . Mean amplitude during training (all groups), post-training in home cage (control group), post-training NE (0.5-hr and 4-hr NE groups), and testing (all groups) [F (4,36)=1.249, p=0.3080]. ( E) . Mean event rate during training (all groups), post-training in home cage (control group), post-training NE (0.5-hr and 4-hr NE groups), and testing (all groups) [F (4,36)=0.07365, p=0.9897]. ( F1) . Ensemble reactivation during post-learning recording [F (2,18)=2.710, p=0.0936]. ( F2) . Ensemble reactivation during testing [F (2,18)=4.852, p=0.0206]. ( F3) . Spearman and Pearson analysis were used to determine correlation between discrimination ratio and % of the learning-associated ensemble reactivation during testing. ( G1) . % of total neurons uniquely detected during NE. ( G2) . % of reactivation of NE-specific neurons during testing. Data are presented as mean +/-SEM (n=7 for each group). Data were analyzed by unpaired t-test ( G1 and G2 ) and two-way ANOVA ( C1, C2, D , and E ) or one-way-ANOVA ( C3, F1 , and F2 ) followed by post-hoc pairwise comparison.

Article Snippet: Raw microendoscopic calcium imaging movies were preprocessed using end-to-end CNMF-E (IDEAS, Inscopix Data Exploration, Analysis, and Sharing) to extract neuronal activity events for downstream analysis.

Techniques: In Vivo, Imaging, Activity Assay, Expressing, Control, Comparison