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Text of the page (random words):
brain windows new tools for peering into the brain brain windows new tools for peering into the brain home about journal club brainstorm philosophy code gcamp6 plasmids at addgene 8 11 2012 gcamp6 variants are on addgene three flavors fast kinetics or big signals bigger responses than ogb 1 some are much bigger the responses to drifting gratings in visual cortex are spectacular sorry no pics for now hopefully the reviewers will be nice so we can all read about it soon still work to be done getting true 1ap resolution when simultaneously imaging large populations of neurons but for single neuron imaging in vivo this has 1ap resolution if you have been waiting for the gcamps that will blow your expectations away these are them from the sfn abstract using structure guided mutagenesis and high throughput screening we increased the fluorescence change in response to single action potentials aps by 10 fold compared to gcamp3 we also accelerated the kinetics by 2 fold these new gecis reliably report single aps in single trials in vivo with near 100 accuracy in the mouse visual cortex we detected 5 fold more visually responsive neurons the sensitivity dynamic range and speed of the new gecis exceed those of the synthetic indicator ogb 1 the improved sensitivity further facilitated reliable measurement of synaptic calcium signals in the dendrites of pyramidal cells and parvabumin pv positive interneurons in vivo hot spots of orientation selective domains can be resolved both in single pyramidal cell spines and small segments of pv cell dendrites these improved gecis will permit a more complete description of neuronal circuit function and enable long term functional imaging of single synapses comments 3 comments tags gcamp6 geci categories calcium in vivo genetically encoded intracellular em stain for connectomics 25 10 2012 the field of connectomics would greatly benefit from a genetically encoded stain for specific proteins that works intracellularly this could be used to provide positive contrast for axon tracts or to identify if a synapse is excitatory inhibitory or neuromodulatory horseradish peroxidase hrp is a classic approach to em staining but does not work in reducing environments such as inside cells several groups ting looger have tried to engineer away the di sulfide bonds of hrp to allow it to work intracellularly but all have failed to maintain activity after removing these bonds an alternative approach minisog from the tsien lab is a genetically encoded tag that can stain via singlet oxygen generation but requires light to activate it in nature biotechnology alice ting s group reports apex a perioxidase that works intracellularly which they then engineered to monomerize and improve staining performance this tool could find extensive use in connectomics of complex brain tissues comments leave a comment tags connectomics em stain categories circuit mapping connectomics electron microscopy neuroanatomy drosophila visual system 24 10 2012 by twitter request click thru for the original resolution of a fellow janelian s nikon small world 4th place prize winner ryan williamson composed the image drosophila melanogaster visual system halfway through pupal development showing retina gold photoreceptor axons blue and brain green 1500x comments 1 comment tags drosophila imaging rentia categories imaging g camp5 is finally published 3 10 2012 the paper on g camp5 has been published optimization of a gcamp calcium indicator for neural activity imaging genetically encoded calcium indicators gecis are powerful tools for systems neuroscience recent efforts in protein engineering have significantly increased the performance of gecis the state of the art single wavelength geci gcamp3 has been deployed in a number of model organisms and can reliably detect three or more action potentials in short bursts in several systems in vivo through protein structure determination targeted mutagenesis high throughput screening and a battery of in vitro assays we have increased the dynamic range of gcamp3 by severalfold creating a family of gcamp5 sensors we tested gcamp5s in several systems cultured neurons and astrocytes mouse retina and in vivo in caenorhabditis chemosensory neurons drosophila larval neuromuscular junction and adult antennal lobe zebrafish retina and tectum and mouse visual cortex signal to noise ratio was improved by at least 2 to 3 fold in the visual cortex two gcamp5 variants detected twice as many visual stimulus responsive cells as gcamp3 by combining in vivo imaging with electrophysiology we show that gcamp5 fluorescence provides a more reliable measure of neuronal activity than its predecessor gcamp3 gcamp5 allows more sensitive detection of neural activity in vivo and may find widespread applications for cellular imaging in general this is the best fully characterized geci available but publication of the paper was repeatedly delayed why because reviewers viewed it as too incremental of an upgrade and not worth publishing in a prominent journal no i m not talking nature or science level when the plasmids are already available a friendly suggestion for authors and future gcamp6 reviewers you can t have it both ways if you want access to the best molecular tools before publication gcamp5 has been available for over a year you cannot turn around and say its not worth publishing because you already have the plasmid multiple post docs spent years of their lives developing and carefully testing this tool they deserve a quality publication for their efforts furthermore the rigorous performance data collected needs to be available to current and future users finally there is no doubt that this will be a highly cited and viewed paper in whatever journal were to publish it our gcamp3 paper already has 182 citations in less than 3 years this may do even better comments 2 comments tags calcium imaging gcamp geci in vivo categories uncategorized three ways of looking at touch coding 20 09 2012 at sfn a block of three posters by myself simon peron and daniel o connor will showcase three ways to approach the problem of touch coding my work on whisker force measurements and single cell and silicon probe based cortical recordings during active objection localization program poster 677 18 kk18 presentation title encoding whisking related variables in the mouse barrel cortex during object localization location hall f j presentation time tuesday oct 16 2012 2 00 pm 3 00 pm authors s a hires d o connor d gutnisky k svoboda janelia farm res campus ashburn va simon peron s work on recording a complete representation of touch using in vivo imaging with new g camp variants during a similar behavior program poster 677 12 kk12 presentation title towards imaging complete representations of whisker touch in the mouse barrel cortex location hall f j presentation time tuesday oct 16 2012 4 00 pm 5 00 pm authors s p peron 1 v iyer 2 z guo 2 t w chen 2 d kim 2 d huber 3 k svoboda 2 daniel o connor s work on constructing synthetic perception of touch and object localization via cortical cell type specific optogenetic stimulation during behavior program poster 677 06 kk6 presentation title neural coding for object location revealed using synthetic touch location hall f j presentation time tuesday oct 16 2012 2 00 pm 3 00 pm authors d h o connor 1 s a hires 1 z guo 1 q q sun 2 d huber 1 k svoboda 1 this is a must see session for people interested in touch coding the whisker system in vivo cortical imaging or synthetic perception via optogenetics i hope to see you there comments leave a comment categories brain imaging calcium circuit mapping in vivo multiphoton neuronal control optogenetics gcamp6 candidate presentations 20 09 2012 the first public presentation of data on candidates for gcamp6 will be presented here this is obviously a big deal for brain imaging reliable detection of single action potentials and synaptic calcium signals using improved genetically encoded calcium indicators t w chen j yu r a kerr v jayaraman l l looger k svoboda d s kim fff77 927 08oct 17 4 00pm 5 00pm and here engineering next generation gcamp calcium indicators using neuron based screening t w chen t j wardill j p hasseman g tsegaye b f fosque e r schreiter b e kimmel r a kerr v jayaraman k svoboda l l looger d s kim ddd38 207 14oct 14 9 00am 10 00am comments 2 comments categories uncategorized where to get new brainwindows content 29 03 2012 it s been pretty quiet around here lately and will likely continue that way for some time brainwindows is not dead just resting experiments paper writing new baby etc however if you still need a fix of brainwindows analysis please follow me andrewhires on twitter if you don t have a twitter account get one it s the easiest way to get published in the library of congress i ll be honing the analysis to fit into 140 character snippets there will also be a much broader range of topics hopefully we can continue a quality scientific discourse publicly in near real time comments 1 comment categories uncategorized gcamp5 is out 15 11 2011 gcamp3 is now officially old skool gcamp5 is available at addgene plasmid 31788 pcmv gcamp5g a k a gcamp3 t302l r303p d380y dimmer baseline f higher df f picks up significantly more activity in vivo cortex still not holy grail level but getting closer comments 15 comments categories calcium cortical encoding of somatosensory input 15 11 2011 wednesday morning i m giving the first public presentation of my current work on sensory coding in the barrel cortex the big picture question is how does the cortex translate sensory input into perception and recognition of objects and their position to study this cortical function we used a methodology with 3 critical components 1 goal directed discrimination task the activity of an awake cortex is profoundly different in character from an anesthetized cortex there is also gathering evidence that the activity of sensory cortex when attending to and using its sensory input to perform a discrimiation is quite diffent from periods of inattention we use a goal directed discrimination task to enforce attention and to ensure the recorded activity is relevant to the fundamental function of the area 2 high speed neural recording techniques spikes are the words in the language of cortex we must record them with high fidelity and temporal precision we can then use correlation of neural activity to sensory input to try to understand what the cells are saying 3 precise measurement of sensory input if we are to use correlational techniques to describe the language of cortex we must match the millisecond precision of cortical communication with millisecond precision in measuring the exact sensory input within the rodent no study has yet combined all three components goal directed discrimination behavior millisecond precision neuronal recordings and millisecond precision sensory input recordings anyway if you want to hear more try to get up in time to make it to the conference by 8 45am program poster 750 04 presentation title encoding of vibrissal sensory input and task related variables in the mouse barrel cortex during whisker based object localization location 152b presentation time wednesday nov 16 2011 8 45 am 9 00 am comments leave a comment categories uncategorized useful chr2 mouse lines 19 08 2011 guoping feng s group has released what looks to be a very useful set of bac transgenic channelrhodopsin mice the four lines specifically express yfp tagged chr2 in gabaergic cholinergic serotonergic and parvalbumin expressing neurons they are well characterized and available from jackson labs comments leave a comment categories uncategorized previous entries lab linker alice ting amy palmer atsushi miyawaki jin zhang karel svoboda lei wang loren looger michael lin oliver griesbeck rob campbell roger tsien science blogs biosingularity brain stimulant brain waves brains lab caged calcium en dogeno us labrigger neurochannels neurodudes nuit blanche on the brain reporter gene ryohei s neuroscience notes scientific clearing house sclin s neuroscience blog post categories atp 2 blogroll 1 brain imaging 14 brainstorm 1 calcium 28 channelrhodopsin 9 circuit mapping 10 commentary 1 computational 1 connectomics 1 consciousness 2 data analysis 3 education 1 electron microscopy 4 electrophysiology 2 entertainment 2 fluorescence 6 fluorescent protein 30 fmri 3 fret 17 fun 7 genetics 4 gfp 7 glutamate 4 imaging 52 in vitro 29 in vivo 41 journal club 2 meeting 9 memory 1 multiphoton 9 neuroanatomy 5 neuronal control 12 optogenetics 5 party 2 personal 1 philosophy 5 photoactivation 7 photobleaching 4 preview 1 quantum dot 1 review 1 san diego 3 science blogs 3 scientific publishing 2 small molecule 3 society for neuroscience 2 software 1 structure 2 super resolution 8 uncategorized 19 video 2 visual cortex 2 visualization 4 voltage 6 web services 1 recent comments forming and recallin on optogenetic induction of memor guixue bu on voltage imaging with sub milli sheryl on voltage sensitive imaging powe sheryl on voltage sensitive imaging powe sheryl on voltage imaging with sub milli blog stats 431 196 hits since march 6th 2007 support brain windows donate bitcoins blog at wordpress com brain windows create a free website or blog at wordpress com subscribe subscribed brain windows join 77 other subscribers sign me up already have a wordpress com account log in now privacy brain windows subscribe subscribed sign up log in report this content view site in reader manage subscriptions collapse this bar loading comments write a comment email required name required website design a site like this with wordpress com get started