ABCDEFGHIJKLMNOPQRSTUVWXYZ
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ZOOM
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Internship Zoom room (pass: 955187)https://harvard.zoom.us/j/98936657730?pwd=T3NQMW9jalhDL3hhd3dGNzNsOENrdz09
Mariela will be in the internship zoom room between 10am and 3pm EST on weekdays with the exception of Tuesday and Friday when she will log in after the Lichtman and Engert lab meetings
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Mariela's Zoom room (pass: zebrafish)https://harvard.zoom.us/my/mpetkova?pwd=RUUvVG92eDltOUMvWXpDMFZMVnJUQT09
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Mariela's calendar (meetings are in Mariela's zoom room)https://marielapetkova.youcanbook.meJust sign on for a meeting time, if the slot shows as available, then it is yours
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Lichtman lab meeting Tuesdays 9am-11am EST
the zoom link changes weekly, it will be posted the morning before the meeting in #zebrafish_em
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Engert lab meeting Fridays 9am-noonish EST (pass: 701015)https://harvard.zoom.us/j/785469688
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RESOURCES
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Zbrain ATLAS 2.0 + EMhttps://zebrafishatlas.zib.de/EM
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Zbrain ATLAS 1.0https://zebrafishexplorer.zib.de/home/
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Histology atlashttp://histologyguide.com/EM-atlas/EM-atlas.html
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Anatomy EM atlashttps://synapseweb.clm.utexas.edu/
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Electron microscopy (Neuroglancer)
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Alignment Jan 2021
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:%5B81566.015625%2C67400.46875%2C3287.5%5D%2C%22crossSectionScale%22:99.98298284927172%2C%22projectionScale%22:524288%2C%22layers%22:%5B%7B%22type%22:%22image%22%2C%22source%22:%22brainmaps://828646373025:fish1:raw_20210108_xyz%22%2C%22tab%22:%22source%22%2C%22name%22:%22raw_20210108_xyz%22%7D%5D%2C%22selectedLayer%22:%7B%22layer%22:%22raw_20210108_xyz%22%2C%22visible%22:true%7D%2C%22layout%22:%224panel%22%7D
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Alignment May 2021
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:%5B88988.5859375%2C69355.2578125%2C2976.5%5D%2C%22crossSectionScale%22:83.57312907691608%2C%22projectionScale%22:524288%2C%22layers%22:%5B%7B%22type%22:%22image%22%2C%22source%22:%22brainmaps://828646373025:fish1:raw_20210501_clahe_xy?chunkLayout=flat%22%2C%22tab%22:%22source%22%2C%22name%22:%22raw_20210501_clahe_xy?chunkLayout=flat%22%7D%5D%2C%22selectedLayer%22:%7B%22visible%22:true%2C%22layer%22:%22raw_20210501_clahe_xy?chunkLayout=flat%22%7D%2C%22layout%22:%22xy%22%7D
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Base segmentation "rc1"
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:%5B88291.109375%2C75008.015625%2C4334.5%5D%2C%22crossSectionOrientation%22:%5B0%2C0%2C0.0023006880655884743%2C-0.9999973773956299%5D%2C%22crossSectionScale%22:43.00164637854132%2C%22projectionScale%22:524288%2C%22layers%22:%5B%7B%22type%22:%22image%22%2C%22source%22:%22brainmaps://828646373025:fish1:raw_20210501_clahe%22%2C%22tab%22:%22source%22%2C%22name%22:%221%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%22brainmaps://828646373025:fish1:raw_20210501_seg_rc1%22%2C%22tab%22:%22source%22%2C%22name%22:%22raw_20210501_seg_rc1%22%7D%5D%2C%22selectedLayer%22:%7B%22visible%22:true%2C%22layer%22:%22raw_20210501_seg_rc1%22%7D%2C%22layout%22:%22xy%22%7D
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[2021] Base segmentation "rc2"
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:%5B88291.109375%2C75008.015625%2C4334.5%5D%2C%22crossSectionOrientation%22:%5B0%2C0%2C0.0023006880655884743%2C-0.9999973773956299%5D%2C%22crossSectionScale%22:43.00164637854132%2C%22projectionScale%22:524288%2C%22layers%22:%5B%7B%22type%22:%22image%22%2C%22source%22:%22brainmaps://828646373025:fish1:raw_20210501_clahe%22%2C%22tab%22:%22source%22%2C%22name%22:%221%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%22brainmaps://828646373025:fish1:raw_20210501_seg_rc1%22%2C%22tab%22:%22source%22%2C%22name%22:%22raw_20210501_seg_rc1%22%2C%22archived%22:true%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%22brainmaps://828646373025:fish1:raw_20210501_seg_rc2%22%2C%22tab%22:%22source%22%2C%22name%22:%22raw_20210501_seg_rc2%22%7D%5D%2C%22selectedLayer%22:%7B%22visible%22:true%7D%2C%22layout%22:%22xy%22%7D
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Agglomeration of "rc2"
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:%5B88291.109375%2C75008.015625%2C4334.5%5D%2C%22crossSectionOrientation%22:%5B0%2C0%2C0.0023006880655884743%2C-0.9999973773956299%5D%2C%22crossSectionScale%22:43.00164637854132%2C%22projectionScale%22:524288%2C%22layers%22:%5B%7B%22type%22:%22image%22%2C%22source%22:%22brainmaps://828646373025:fish1:raw_20210501_clahe%22%2C%22tab%22:%22source%22%2C%22name%22:%221%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%22brainmaps://828646373025:fish1:raw_20210501_seg_rc1%22%2C%22tab%22:%22source%22%2C%22name%22:%22raw_20210501_seg_rc1%22%2C%22archived%22:true%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%22brainmaps://828646373025:fish1:raw_20210501_seg_rc2:agg20210618%22%2C%22tab%22:%22source%22%2C%22name%22:%22agglomeration_210618%22%7D%5D%2C%22selectedLayer%22:%7B%22visible%22:true%2C%22layer%22:%22agglomeration_210618%22%7D%2C%22layout%22:%22xy%22%7D
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[2022] Base segmentation
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:%5B52171.76953125%2C32408.541015625%2C6294.90478515625%5D%2C%22crossSectionScale%22:60.10632710591174%2C%22projectionOrientation%22:%5B0.29750484228134155%2C-0.05198398232460022%2C-0.016357911750674248%2C0.9531636834144592%5D%2C%22projectionScale%22:9721.053129639591%2C%22layers%22:%5B%7B%22type%22:%22image%22%2C%22source%22:%22brainmaps://828646373025:fish1:raw_20211023_clahe%22%2C%22tab%22:%22source%22%2C%22name%22:%22raw_20211023_clahe%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%22brainmaps://828646373025:fish1:raw_20211023_seg_20220521%22%2C%22tab%22:%22source%22%2C%22name%22:%22raw_20211023_seg_20220521%22%7D%5D%2C%22layout%22:%22xy%22%7D
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[2022] Agglomeration1
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:%5B53931.859375%2C33991.08203125%2C4870.5%5D%2C%22crossSectionScale%22:36.67146386936077%2C%22projectionOrientation%22:%5B-0.15656918287277222%2C-0.4431052505970001%2C-0.8086321949958801%2C-0.35391783714294434%5D%2C%22projectionScale%22:19313.516541827816%2C%22layers%22:%5B%7B%22type%22:%22image%22%2C%22source%22:%22brainmaps://828646373025:fish1:raw_20211023_clahe%22%2C%22tab%22:%22source%22%2C%22name%22:%22raw_20211023_clahe%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%22brainmaps://828646373025:fish1:raw_20211023_seg_20220521:220623_8_spl%22%2C%22tab%22:%22source%22%2C%22name%22:%22agglo32_16_8%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%22brainmaps://828646373025:fish1:raw_20211023_seg_20220521:220531_8_spl%22%2C%22tab%22:%22source%22%2C%22segments%22:%5B%224403962694%22%2C%224430490753%22%2C%224439315796%22%2C%224439329623%22%5D%2C%22name%22:%22220531_8_spl%22%2C%22archived%22:true%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%22brainmaps://828646373025:fish1:raw_20211023_seg_20220521:220531_16_spl%22%2C%22tab%22:%22source%22%2C%22segments%22:%5B%227453263105%22%5D%2C%22name%22:%22220531_16_spl%22%2C%22archived%22:true%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%22brainmaps://828646373025:fish1:raw_20211023_seg_20220521:220623_16_spl%22%2C%22tab%22:%22source%22%2C%22segments%22:%5B%228637660077%22%5D%2C%22name%22:%22220623_32_spl%22%2C%22archived%22:true%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%22brainmaps://828646373025:fish1:raw_20211023_seg_20220521:220623_16_spl%22%2C%22tab%22:%22source%22%2C%22name%22:%22agglo32_16%22%2C%22visible%22:false%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%22brainmaps://828646373025:fish1:raw_20211023_seg_20220521:220623_32_spl%22%2C%22tab%22:%22source%22%2C%22name%22:%22agglo32%22%2C%22visible%22:false%7D%5D%2C%22selectedLayer%22:%7B%22visible%22:true%2C%22layer%22:%22raw_20211023_clahe%22%7D%2C%22layout%22:%22xy%22%7D
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Somas from low-res images
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:%5B118652.421875%2C71713.59375%2C5308.5%5D%2C%22crossSectionScale%22:15.468693665127788%2C%22projectionScale%22:491519.99999999994%2C%22layers%22:%5B%7B%22type%22:%22image%22%2C%22source%22:%22brainmaps://828646373025:fish1:raw_20210501_clahe%22%2C%22tab%22:%22source%22%2C%22name%22:%22raw_20210501_clahe%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%22brainmaps://828646373025:fish1:raw_20210501_lores_somas%22%2C%22tab%22:%22segments%22%2C%22name%22:%22somas%22%7D%5D%2C%22selectedLayer%22:%7B%22visible%22:true%2C%22layer%22:%22somas%22%7D%2C%22layout%22:%22xy%22%7D
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TUTORIALS
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Electron microscopy for connectomics
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Mariela's PhD defense (video)https://www.dropbox.com/s/toyep3yffe93aru/zoom_0.mp4?dl=0
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Mariela's dissertation (text)https://dash.harvard.edu/handle/1/37365549?show=full
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Jeff Lichtman "Connectomics: What, Why and How?"https://www.youtube.com/watch?v=PRJPXJL3Np0
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Synapse training
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ManualLINK
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Synapse Labeling Training Tool & DATALINK
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Synapse labeling trainig tool tutorialLINK
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Synapse labeling testing tool tutorialLINK
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Brain mapping
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Brain mapping 101https://science.eyewire.org/home
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Play eyewirehttps://eyewire.org/
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Agglo training
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Neuroglancer - navigation control quick demohttps://www.dropbox.com/s/sbcktjueqiv2upc/NeuroglancerDemo.mp4?dl=0
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Agglomeration and segmentation - what is it?
https://docs.google.com/document/d/1v6BnRm5GrYwP544U_JUlnEeUHhGNtyhrSMbPy4SmddE/edit?usp=sharing
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Neuroglancer - what are all the parts?
https://docs.google.com/presentation/d/1E-2EhKCHlQSakkJR7yu4oP2LXQIPS5Pql7XeMedjPp8/edit?usp=sharing
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Agglomeration examples
https://docs.google.com/spreadsheets/d/16RH49ZH6V9yJQLhkSgt2XtrPzNUsDAAZs6r_lCDVo2s/edit?usp=sharing
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Empty workspace for base segmentation rc2
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:%5B97514.5%2C86648.5%2C5866.5%5D%2C%22crossSectionScale%22:1.2985372034837654%2C%22projectionOrientation%22:%5B0.591366708278656%2C0.0947895348072052%2C-0.1521177440881729%2C0.7862318754196167%5D%2C%22projectionScale%22:43036.17975852668%2C%22layers%22:%5B%7B%22type%22:%22image%22%2C%22source%22:%22brainmaps://828646373025:fish1:raw_20210501_clahe%22%2C%22tab%22:%22source%22%2C%22name%22:%22EM%20images%20%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%22brainmaps://828646373025:fish1:raw_20210501_seg_rc1%22%2C%22tab%22:%22source%22%2C%22name%22:%22raw_20210501_seg_rc1%22%2C%22archived%22:true%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%22brainmaps://828646373025:fish1:raw_20210501_seg_rc2%22%2C%22tab%22:%22segments%22%2C%22colorSeed%22:264334123%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:%22annotateSphere%22%2C%22tab%22:%22annotations%22%2C%22annotationColor%22:%22#ffffff%22%2C%22annotations%22:%5B%5D%2C%22name%22:%22Annotations%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:%22wtf%22%7D%5D%2C%22showSlices%22:false%2C%22selectedLayer%22:%7B%22visible%22:true%2C%22layer%22:%22wtf%22%7D%2C%22layout%22:%22xy-3d%22%2C%22selection%22:%7B%22layers%22:%7B%22Annotations%22:%7B%22annotationId%22:%222b41a514454bd2bc6d50241df97a57324cb1a4f8%22%2C%22annotationSource%22:0%2C%22annotationSubsource%22:%22default%22%7D%7D%7D%7D
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How to find cell locations in full res images from cellID in low res
https://www.dropbox.com/s/vxfukvbq54lir80/How_to_find_cells_from_lores_to_high_res.mp4?dl=0
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EVENTS
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INVITED SPEAKERS (MONDAYS 11am - 12:30pm EST)
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Jun 14Welcome/Orientation/Meet everyone
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Jun 21Thomas Gregor, Princeton University & Institute Pasteur - Fly development
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Jun 28Rob Philips, Caltech University & Christina Hueschen, Stanford University
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Jul 5Avital Rodal, Brandeis University - Dynamic picture of neurons
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Jul 12Farhana Akter MD, Harvard University - Being a scientists and a physician
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Jul 19Nate Sawtell, Columbia University - Electric fish
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Jul 26No speaker (NIH site visit dress rehearsal - all welcome)
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Aug 2Florian Engert - U19 Brain initiative
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Aug 9Paul Katz, UMass Amherst
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WORKSHOPS (WEDNESDAYS 11am - 1pm EST)
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Jun 16Are we ready to go? Is everything installed? Are all the links working?
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Checklist for week1
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Jun 23Neuroglancer intro Pt1. Giving science talks and writing scientifically
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Checklist for week2
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Jun 30Lightning talks tryout - group I
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Jul 7Lightning talks tryout - group II
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Jul 14Writing workshop I (writeups)
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Slides
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Jul 21Lightning talks - Everyone
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Jul 28Lightning talks - Everyone
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Aug 4Roundable with Florian & Jeff
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Aug 11Workshop week (individual meetings)
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PRESENTATIONS
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Jul 29U19 NIH Site visit
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Aug 3Presentation @ Lichtman Lab Meeting
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Aug 13Team presentation @ Engert Lab Meeting
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STRUCTURE+FUNCTION TEAMS
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STUDENTFUNCTION CO-MENTORSPECIFIC PROJECTBROAD PICTURE
PAPER REFERENCE
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Lucy Chen Kristian&MarielaCharacterizing the anterior lateral line inputs. Role of lateral line in salt and mechanosensation
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Dita BerlineKristian&MarielaCharacterizing the anterior lateral line inputs. Role of lateral line in salt and mechanosensation
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Sara RenKristianConnections between slow hindbrain GABA and thalmaus glutamatergicHow does past experience shape behavioral responsiveness
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Christopher Meng Mark Fishman/Florian/Misha Ahrens/Virginia/Kristian/LuisCharacterize Vagal Ganglion Autonomous nervous system and homeostasis
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Boyi FeiMark Fishman/Florian/Misha Ahrens/Virginia/Kristian/LuisCharacterize Vagal Ganglion Autonomous nervous system and homeostasis
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Sharon Deng (flexible time)GregorHindbrain Integrator CircuitTest a circuit model for evidence integration and decision making
https://www.nature.com/articles/s41593-019-0534-9
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Chris (Ruohong) Wang GregorHindbrain Integrator CircuitTest a circuit model for evidence integration and decision making
https://www.nature.com/articles/s41593-019-0534-9
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Josh Hillers HalehMauthner Cell and dopaminergic neural modulation over escape behaviorTest circuit models for escape behavior in zebrafish
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4742414/
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Andew Parisi ClemensArborization fields, collateralsVisual processing in zebrafish
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Stella Gu (full/flexible time)ClemensArborization fields, collateralsVisual processing in zebrafish
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Erin Kim ClemensArborization fields, collateralsVisual processing in zebrafish
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Mo Re Kim (flexible time)ClemensArborization fields, collateralsVisual processing in zebrafish
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Nicholas ParcharidisMariela&AnqiEfferent circuit for motion self-cancellation in the lateral lineDifferentiating between self-caused and externally caused stimuli
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Julian Wagner Carena Mariela&AnqiCurl DetectorTest a circuit model for mechanosensory basis of rheotaxis - how fish swim upstream even in darkness
https://www.nature.com/articles/nature23014
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David Aley SumitCharacterize the structure of E/I cellsCan we tell if a cell is E or I from its morphology?
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Mingyu Zhu (end of June/beginning of July)Misha Ahrens/Alex ChenL-MO GABAergic passivity cells and NE-Mo cellsTest a circuit model for evidence accumulation for "learned helplessness"
https://www.sciencedirect.com/science/article/pii/S009286741930621X
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Anqi YuMisha Ahrens/Alex ChenInferior olive (IO) - cerebellar - Nucleus prepositus hypoglossi (NPH) Test a circuit model for temporal integration during optomotor response (OMR)
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Stacy Jeong (summer full/flexible time)Alex ChenInferior olive (IO) - cerebellar - Nucleus prepositus hypoglossi (NPH) Characterize a cerebellum-like structure specific to fish
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Jasmine MacalandaNagComparative analysis of cerebellum in zebrafish and mice
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