ABCDEFGHIJKLMNOPQRSTUVWXYZAAABACAD
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Data
2
Fish2.0 base seg
https://neuroglancer-demo.appspot.com/#!%7B%22dimensions%22:%7B%22x%22:%5B8e-9%2C%22m%22%5D%2C%22y%22:%5B8e-9%2C%22m%22%5D%2C%22z%22:%5B3e-8%2C%22m%22%5D%7D%2C%22position%22:%5B81625.8984375%2C54551.62890625%2C5859.50048828125%5D%2C%22crossSectionOrientation%22:%5B0%2C0%2C0.04158664122223854%2C-0.99913489818573%5D%2C%22crossSectionScale%22:95.51535815187849%2C%22projectionOrientation%22:%5B-0.5087847709655762%2C0.09280183166265488%2C0.4596307575702667%2C-0.7219871282577515%5D%2C%22projectionScale%22:40455.67504456095%2C%22layers%22:%5B%7B%22type%22:%22image%22%2C%22source%22:%7B%22url%22:%22brainmaps://284407298309:fish2:sofima_240112_xyz%22%2C%22subsources%22:%7B%22default%22:true%7D%2C%22enableDefaultSubsources%22:false%7D%2C%22tab%22:%22source%22%2C%22name%22:%22sofima_240112_xyz%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%7B%22url%22:%22brainmaps://284407298309:fish2:sofima_240112_seg_240529_97033236_2060fbg_1506fbg_1m_zero%22%2C%22subsources%22:%7B%22default%22:true%2C%22/mesh%22:true%7D%2C%22enableDefaultSubsources%22:false%7D%2C%22tab%22:%22segments%22%2C%22selectedAlpha%22:0.35%2C%22segments%22:%5B%5D%2C%22colorSeed%22:4007410884%2C%22name%22:%22base%20segmentation%22%7D%2C%7B%22type%22:%22annotation%22%2C%22source%22:%7B%22url%22:%22local://annotations%22%2C%22transform%22:%7B%22outputDimensions%22:%7B%22x%22:%5B8e-9%2C%22m%22%5D%2C%22y%22:%5B8e-9%2C%22m%22%5D%2C%22z%22:%5B3e-8%2C%22m%22%5D%7D%7D%7D%2C%22tool%22:%22annotatePoint%22%2C%22tab%22:%22rendering%22%2C%22annotationColor%22:%22#71ee68%22%2C%22annotations%22:%5B%5D%2C%22name%22:%22ENDS%22%7D%2C%7B%22type%22:%22annotation%22%2C%22source%22:%7B%22url%22:%22local://annotations%22%2C%22transform%22:%7B%22outputDimensions%22:%7B%22x%22:%5B8e-9%2C%22m%22%5D%2C%22y%22:%5B8e-9%2C%22m%22%5D%2C%22z%22:%5B3e-8%2C%22m%22%5D%7D%7D%7D%2C%22tool%22:%22annotatePoint%22%2C%22tab%22:%22rendering%22%2C%22annotationColor%22:%22#ffae00%22%2C%22annotations%22:%5B%5D%2C%22name%22:%22HELP%21%22%7D%5D%2C%22showAxisLines%22:false%2C%22showSlices%22:false%2C%22selectedLayer%22:%7B%22size%22:318%2C%22visible%22:true%2C%22layer%22:%22base%20segmentation%22%7D%2C%22layout%22:%22xy-3d%22%2C%22selection%22:%7B%22size%22:318%7D%7D
3
Brain volume: Intermediate post-cleaved agglo
https://neuroglancer-demo.appspot.com/#!%7B%22dimensions%22:%7B%22x%22:%5B8e-9%2C%22m%22%5D%2C%22y%22:%5B8e-9%2C%22m%22%5D%2C%22z%22:%5B3e-8%2C%22m%22%5D%7D%2C%22position%22:%5B59304.7578125%2C47118.890625%2C5859.31494140625%5D%2C%22crossSectionOrientation%22:%5B0%2C0%2C0.04158664122223854%2C-0.99913489818573%5D%2C%22crossSectionScale%22:1.1216967460091272%2C%22projectionOrientation%22:%5B-0.4628196358680725%2C0.15612250566482544%2C0.8506216406822205%2C-0.19459332525730133%5D%2C%22projectionScale%22:54635.69531099913%2C%22layers%22:%5B%7B%22type%22:%22image%22%2C%22source%22:%7B%22url%22:%22brainmaps://284407298309:fish2:sofima_240112_xyz%22%2C%22subsources%22:%7B%22default%22:true%7D%2C%22enableDefaultSubsources%22:false%7D%2C%22tab%22:%22source%22%2C%22name%22:%22sofima_240112_xyz%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%7B%22url%22:%22brainmaps://284407298309:fish2:sofima_240112_seg_240529_97033236_2060fbg_1506fbg_1m_zero%22%2C%22subsources%22:%7B%22default%22:true%2C%22/mesh%22:true%7D%2C%22enableDefaultSubsources%22:false%7D%2C%22tab%22:%22rendering%22%2C%22selectedAlpha%22:0.35%2C%22segments%22:%5B%5D%2C%22colorSeed%22:4007410884%2C%22segmentDefaultColor%22:%22#f5d60a%22%2C%22name%22:%22BASE%22%2C%22visible%22:false%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%7B%22url%22:%22brainmaps://284407298309:fish2:sofima_240112_seg_240529_97033236_2060fbg_1506fbg_1m_zero_grid1k:20250322_ddeda8_fixsv2%22%2C%22subsources%22:%7B%22default%22:true%2C%22/mesh%22:true%7D%2C%22enableDefaultSubsources%22:false%7D%2C%22tab%22:%22segments%22%2C%22selectedAlpha%22:0.35%2C%22segments%22:%5B%5D%2C%22colorSeed%22:4007410884%2C%22name%22:%22AGGLO%22%7D%2C%7B%22type%22:%22annotation%22%2C%22source%22:%7B%22url%22:%22local://annotations%22%2C%22transform%22:%7B%22outputDimensions%22:%7B%22x%22:%5B8e-9%2C%22m%22%5D%2C%22y%22:%5B8e-9%2C%22m%22%5D%2C%22z%22:%5B3e-8%2C%22m%22%5D%7D%7D%7D%2C%22tool%22:%22annotatePoint%22%2C%22tab%22:%22annotations%22%2C%22annotationColor%22:%22#ee68ea%22%2C%22annotations%22:%5B%5D%2C%22name%22:%22ends%22%7D%2C%7B%22type%22:%22annotation%22%2C%22source%22:%7B%22url%22:%22local://annotations%22%2C%22transform%22:%7B%22outputDimensions%22:%7B%22x%22:%5B8e-9%2C%22m%22%5D%2C%22y%22:%5B8e-9%2C%22m%22%5D%2C%22z%22:%5B3e-8%2C%22m%22%5D%7D%7D%7D%2C%22tool%22:%22annotatePoint%22%2C%22tab%22:%22annotations%22%2C%22annotationColor%22:%22#ffae00%22%2C%22annotations%22:%5B%5D%2C%22name%22:%22help%22%7D%2C%7B%22type%22:%22annotation%22%2C%22source%22:%7B%22url%22:%22local://annotations%22%2C%22transform%22:%7B%22outputDimensions%22:%7B%22x%22:%5B8e-9%2C%22m%22%5D%2C%22y%22:%5B8e-9%2C%22m%22%5D%2C%22z%22:%5B3e-8%2C%22m%22%5D%7D%7D%7D%2C%22tool%22:%22annotatePoint%22%2C%22tab%22:%22annotations%22%2C%22annotationColor%22:%22#44ff00%22%2C%22annotations%22:%5B%5D%2C%22name%22:%22axon%22%7D%2C%7B%22type%22:%22annotation%22%2C%22source%22:%7B%22url%22:%22local://annotations%22%2C%22transform%22:%7B%22outputDimensions%22:%7B%22x%22:%5B8e-9%2C%22m%22%5D%2C%22y%22:%5B8e-9%2C%22m%22%5D%2C%22z%22:%5B3e-8%2C%22m%22%5D%7D%7D%7D%2C%22tool%22:%22annotatePoint%22%2C%22tab%22:%22annotations%22%2C%22annotationColor%22:%22#ff0000%22%2C%22annotations%22:%5B%5D%2C%22name%22:%22merge%20error%22%7D%5D%2C%22showSlices%22:false%2C%22selectedLayer%22:%7B%22size%22:161%2C%22visible%22:true%2C%22layer%22:%22AGGLO%22%7D%2C%22layout%22:%22xy-3d%22%2C%22selection%22:%7B%22size%22:161%2C%22layers%22:%7B%22axon%22:%7B%22annotationId%22:%22f04f9f6268594a7ff92e9278ac6de027a739005e%22%2C%22annotationSource%22:0%2C%22annotationSubsource%22:%22default%22%7D%7D%7D%7D
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Most current CLIO stateCLIO
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Colab code for interacting with Neuprint
https://colab.research.google.com/drive/11P5eV728qJQZWH7eK0Q3UnUtfzTQzjid?usp=sharing
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Colab code for fetching synapse locations
https://colab.research.google.com/drive/12b6juifxGx6wFZoFvfzFucXMZ0SfC68V?usp=sharing
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Reconstructions and help desk
https://docs.google.com/spreadsheets/d/1ekd_ckCiE9vu1q2sfMBj0WT0Gk1nrgafY7Hv5LyvyY0/edit?usp=sharing
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Flagging merge errors
https://docs.google.com/spreadsheets/d/1XlCRXyzrXQHMbZ6DgoE_4YO-FqP1x4e4ykiOsx81tFs/edit?usp=sharing
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Body volume + brain volume
https://neuroglancer-demo.appspot.com/#!%7B%22dimensions%22:%7B%22x%22:%5B8e-9%2C%22m%22%5D%2C%22y%22:%5B8e-9%2C%22m%22%5D%2C%22z%22:%5B3e-8%2C%22m%22%5D%7D%2C%22position%22:%5B89010.0625%2C44119.8046875%2C9766.3212890625%5D%2C%22crossSectionScale%22:189.61581522951948%2C%22projectionOrientation%22:%5B-0.028491998091340065%2C0.6722739338874817%2C0.739391028881073%2C-0.02316967025399208%5D%2C%22projectionScale%22:35477.3324887786%2C%22layers%22:%5B%7B%22type%22:%22image%22%2C%22source%22:%7B%22url%22:%22gs+ngauth+https://ngauth-goog.appspot.com/fish2-heart/em_feabas_20250328/%7Cneuroglancer-precomputed:%22%2C%22transform%22:%7B%22matrix%22:%5B%5B1%2C0%2C0%2C0%5D%2C%5B0%2C1%2C0%2C0%5D%2C%5B0%2C0%2C1%2C10253%5D%5D%2C%22outputDimensions%22:%7B%22x%22:%5B8e-9%2C%22m%22%5D%2C%22y%22:%5B8e-9%2C%22m%22%5D%2C%22z%22:%5B3e-8%2C%22m%22%5D%7D%7D%7D%2C%22tab%22:%22rendering%22%2C%22opacity%22:1%2C%22name%22:%22em_feabas_20250328%22%7D%2C%7B%22type%22:%22image%22%2C%22source%22:%22brainmaps://284407298309:fish2:sofima_240112_xyz%22%2C%22tab%22:%22rendering%22%2C%22opacity%22:0.78%2C%22name%22:%22sofima_240112_xyz%22%7D%5D%2C%22showSlices%22:false%2C%22layout%22:%224panel-alt%22%7D
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Preliminary CLEM
https://neuroglancer-demo.appspot.com/#!%7B%22dimensions%22:%7B%22x%22:%5B5.12e-7%2C%22m%22%5D%2C%22y%22:%5B5.12e-7%2C%22m%22%5D%2C%22z%22:%5B4.8e-7%2C%22m%22%5D%7D%2C%22position%22:%5B918.5515747070312%2C497.5729675292969%2C271.5%5D%2C%22crossSectionScale%22:1.101352529439511%2C%22projectionScale%22:4369.0666666666675%2C%22layers%22:%5B%7B%22type%22:%22image%22%2C%22source%22:%7B%22url%22:%22brainmaps://284407298309:fish2:sofima_240112_xyz%22%2C%22transform%22:%7B%22matrix%22:%5B%5B1%2C0%2C0%2C-330%5D%2C%5B0%2C1%2C0%2C-300%5D%2C%5B0%2C0%2C1%2C0%5D%5D%2C%22outputDimensions%22:%7B%22x%22:%5B5.12e-7%2C%22m%22%5D%2C%22y%22:%5B5.12e-7%2C%22m%22%5D%2C%22z%22:%5B4.8e-7%2C%22m%22%5D%7D%7D%7D%2C%22tab%22:%22source%22%2C%22name%22:%22sofima_240112_xyz%22%2C%22archived%22:true%7D%2C%7B%22type%22:%22image%22%2C%22source%22:%22brainmaps://284407298309:fish2:clem_250519_em_inverted231109_512nm_crop_x330_y300%22%2C%22tab%22:%22source%22%2C%22name%22:%22clem_250519_em_inverted231109_512nm_crop_x330_y300%22%7D%2C%7B%22type%22:%22image%22%2C%22source%22:%22brainmaps://284407298309:fish2:clem_250519_lsfm_in_em_cropped%22%2C%22tab%22:%22rendering%22%2C%22shader%22:%22#uicontrol%20invlerp%20normalized%5Cnvoid%20main%28%29%20%7B%5Cn%20%20emitRGB%28vec3%280.0%2C%20normalized%28%29%2C%200.0%29%29%3B%5Cn%7D%5Cn%22%2C%22shaderControls%22:%7B%22normalized%22:%7B%22range%22:%5B1265%2C40500%5D%2C%22window%22:%5B0%2C50386%5D%7D%7D%2C%22name%22:%22lsfm%22%2C%22visible%22:false%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%22brainmaps://284407298309:fish2:clem_250519_zapbench_in_em_cropped%22%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22name%22:%22zapbench_seg%22%7D%2C%7B%22type%22:%22image%22%2C%22source%22:%22brainmaps://284407298309:fish2:clem_250519_confocal_in_em_cropped%22%2C%22tab%22:%22rendering%22%2C%22shader%22:%22#uicontrol%20invlerp%20normalized%5Cnvoid%20main%28%29%20%7B%5Cn%20%20emitRGB%28vec3%28normalized%28%29%2C%200.0%2C%200.0%29%29%3B%5Cn%7D%5Cn%22%2C%22shaderControls%22:%7B%22normalized%22:%7B%22range%22:%5B0%2C88658.10727338702%5D%2C%22window%22:%5B-14892.700434374721%2C103550.80770776175%5D%7D%7D%2C%22name%22:%22confocal%22%2C%22visible%22:false%7D%5D%2C%22layout%22:%22xy%22%7D
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Lateral line project 🐠
https://docs.google.com/spreadsheets/d/1ePufHL-QHqsqEZ6cuts9VQavvvTLLhd483BodjTt8xc/edit?usp=sharing
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Useful links
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fish2
https://neuroglancer-demo.appspot.com/#!%7B%22dimensions%22:%7B%22x%22:%5B8e-9%2C%22m%22%5D%2C%22y%22:%5B8e-9%2C%22m%22%5D%2C%22z%22:%5B3e-8%2C%22m%22%5D%7D%2C%22position%22:%5B81625.8984375%2C54551.62890625%2C5859.50048828125%5D%2C%22crossSectionOrientation%22:%5B0%2C0%2C0.04158664122223854%2C-0.99913489818573%5D%2C%22crossSectionScale%22:95.51535815187849%2C%22projectionOrientation%22:%5B-0.5087847709655762%2C0.09280183166265488%2C0.4596307575702667%2C-0.7219871282577515%5D%2C%22projectionScale%22:40455.67504456095%2C%22layers%22:%5B%7B%22type%22:%22image%22%2C%22source%22:%7B%22url%22:%22brainmaps://284407298309:fish2:sofima_240112_xyz%22%2C%22subsources%22:%7B%22default%22:true%7D%2C%22enableDefaultSubsources%22:false%7D%2C%22tab%22:%22source%22%2C%22name%22:%22sofima_240112_xyz%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%7B%22url%22:%22brainmaps://284407298309:fish2:sofima_240112_seg_240529_97033236_2060fbg_1506fbg_1m_zero%22%2C%22subsources%22:%7B%22default%22:true%2C%22/mesh%22:true%7D%2C%22enableDefaultSubsources%22:false%7D%2C%22tab%22:%22segments%22%2C%22selectedAlpha%22:0.72%2C%22segments%22:%5B%5D%2C%22colorSeed%22:4007410884%2C%22name%22:%22base%20segmentation%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%22brainmaps://284407298309:fish2:sofima_240112_seg_240529_97033236_2060fbg_1506fbg_1m_zero:240629_rsg5u_t10k_p075_spl%22%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22name%22:%22agglomeration%22%7D%5D%2C%22showAxisLines%22:false%2C%22showSlices%22:false%2C%22selectedLayer%22:%7B%22size%22:354%2C%22layer%22:%22agglomeration%22%7D%2C%22layout%22:%22xy-3d%22%2C%22selection%22:%7B%22size%22:354%7D%7D
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Papers
https://www.dropbox.com/scl/fo/2ruvuv7lukr3mkfg4zdig/AMRRQcRE_PVmT0hOJ3loIBM?rlkey=q92keof9g37c3i25zm4ct04gp&dl=0
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ZapBenchhttps://zapbench-release.storage.googleapis.com/landing.html#results
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Zbrain atlashttps://zebrafishatlas.zib.de/
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Fish1 releasehttps://fish1-release.storage.googleapis.com/gallery.html
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Projects
https://docs.google.com/document/d/1ANHtpU839Ltb65g32e3auo37ZsfCPPl1ef5c3zveAAE/edit?usp=sharing
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Mariela's zoom room
https://harvard.zoom.us/my/mpetkova?pwd=RUUvVG92eDltOUMvWXpDMFZMVnJUQT09
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Useful reading
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Does your mother know?
https://www.dropbox.com/scl/fi/cddfjy9qnzfi67z9jviud/Does_your_mother_know.pdf?rlkey=9j9h67mkkbbnrxofrzoi7453s&st=7fqj2s83&dl=0
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CommesWorkshop
https://www.dropbox.com/scl/fi/k1lu4av1cv1lzo1kxzru6/CommsWorkshop.pptx?rlkey=je4fu0iw8un68mkc9n7n5lcch&dl=0
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Schedule stuff
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Week1 introduction to proofreading, proofreading in teams
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Week2proofreading individually + Mariela support; hear about projects from mentors
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18/Jun, Weds: 11:30am Alex + Yasuko
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18/Jun, Weds: 2:30pm Marc
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19/Jun holiday
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20/Jun 2:30pm Vickie Wangmoved to next week
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Week3more practice, hear about projects from mentors, pick a project + mentor
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23/Jun, Monday 10:30am Kristian-Sachar-Luis
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Week4work on individual projects, begin project presentation practice
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Jun 30 11am-12pm, MonLily, Isaac present
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July 1st 11am-12pm, TuesAyaan, Zoe present
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July 2nd 11am-12pm, WedsBen, Shikha, Kaden present
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Mariela out July 3rd, then its July 4th long weekend
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Week5-9Invited speakers + project presentations every week or every other week.
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July 7thHigh school students join us, welcome!
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July 9th, 10am, WedesdayJane Kondev
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July 10th, 10:30am, ThursdayVickie Wang
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July11th, 9am Engert lab meeting Kristian Herrera
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July11th, noon, Lichtman lab meeting Simone Rey
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July 14th, 10:30am, Mon3 people present
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July 15th, 10:30am, Tuesday3 people present
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July 16th, 10:30 am, Wednesday 3 people present
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July 17th, 10:30 am, Thursday Yasuko Isoe
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July 18th, 9 am, Engert Lab MeetingMisha Ahrens (Janelia)
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July 22nd, 11am, TuesdayMichał Januszewski (Google)
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July 25th, 9am, Engert Lab Meetinglab members weekly update slides
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July 28th, 10:30am, Monopen mic
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July 30th, 10:30, WedsVagus team
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July 31st 10:30 am, ThursAction team
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Aug 5th, 10:30am, TuesOpen mic
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Aug 6th, 10:30am, WednesdayTing Ting Yan
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Aug 7th, 10:30am, Thursdaysend the final presentation slide deck to Mariela
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Aug 7th, 1pm, Thursday, NW 253Jeff Lichtman
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Aug 8th, 9am -- SCION FINAL PRESENTATIONS
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