Synaptome Stats – Lab Notebooks

MEDA runs

Current State of MEDA

Collman data runs on manually labeled synapses

• collman15v2 tight vs 11^3 on annotations
• collman15v2 Gaba classifications on tight annotation
• collman15v2 Gaba classifications on max of 361x361x11 cube
• collman15v2 Gaba classifications on max of 361x361x11 cube without DAPI
• collman14v2 tight annotations
  • top 5 synaptograms per cluster
• collman14v2 GaussianWeighted annotations
  • top 5 synaptograms per cluster
  • XYZ plots

RORB Notebooks

• RORB: Avg over 11x11x11 ~~ 0.61 microns^3
• RORB: Max over 11x11x11 ~~ 0.61 microns^3
• RORB: Gaussian Avg. over 11x11x11 ~~ 0.61 microns^3
• RORB: NOMADS detections with Gaussian Avg. over 11x11x11 ~~ 0.61 microns^3
• RORB: isomap on Gaussian Avg over 11x11x11 ~~ 0.61 microns^3
• RORB: isomap w/o DAPI and MBP on Gaussian Avg over 11x11x11 ~~ 0.61 microns^3
• RORB: tsne on Gaussian Avg over 11x11x11 ~~ 0.61 microns^3
• RORB: Unsupervised RandomForest on Gaussian Avg over 11x11x11 ~~ 0.61 microns^3
• RORB: Unsupervised RandomForest on Gaussian Avg over 11x11x11 ~~ 0.61 microns^3 without DAPI and MBP
• RORB: step-wise regression on Gaussian Avg over 11x11x11 ~~ 0.61 microns^3
• RORB: (Sum(inh), Sum(ex)) on Gaussian Avg over 11x11x11 ~~ 0.61 microns^3
• RORB: \(\hat{L}\) Exploration on Gaussian Avg over 11x11x11 ~~ 0.61 microns^3
• RORB: Shaft v PSD95
• RORB: NMF
• RORB: annuli stats

Early Explorations

• Feature Exploration
• Marker Exploration
• Synapse Exploration
  • Lin F0
  • Log F0
  • Lin F1
  • Log F1

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Progress Reports

• June 2017 Notes
• July 2017 Notes
• August 2017 Notes
• Y3 Progress Report
• Y2 Progress Report

Initial Work

• Initial work by Youngser Park
• Clustering with PAMK and K-Means
• Correlation matrices on a random half