Large-scale, case-control genome-wide association studies (GWASs) have revealed genetic variations associated with diverse neurological and psychiatric disorders. Recent advances in neuroimaging and genomic databases of large healthy and diseased cohorts have empowered studies to characterize effects of the discovered genetic factors on brain structure and function, implicating neural pathways and genetic mechanisms in the underlying biology. However, the unprecedented scale and complexity of the imaging and genomic data requires new advanced biomedical data science tools to manage, process and analyze the data. In this work, we introduce Neuroimaging PheWAS (phenome-wide association study): a web-based system for searching over a wide variety of brain-wide imaging phenotypes to discover true system-level gene-brain relationships using a unified genotype-to-phenotype strategy. This design features a user-friendly graphical user interface (GUI) for anonymous data uploading, study definition and management, and interactive result visualizations as well as a cloud-based computational infrastructure and multiple state-of-art methods for statistical association analysis and multiple comparison correction. We demonstrated the potential of Neuroimaging PheWAS with a case study analyzing the influences of the apolipoprotein E (APOE) gene on various brain morphological properties across the brain in the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort. Benchmark tests were performed to evaluate the system's performance using data from UK Biobank. The Neuroimaging PheWAS system is freely available. It simplifies the execution of PheWAS on neuroimaging data and provides an opportunity for imaging genetics studies to elucidate routes at play for specific genetic variants on diseases in the context of detailed imaging phenotypic data.
Figure 3. Example visualizations generated from the GUI including raster plots, time-series traces, LFP activity peaks, and time frequency transformations. (A) 407 channels selected for this analysis representing the MEA sensor spatial array, covering both the neocortex and the hippocampal regions. (B) Raster plot for all the channels in the working file irrespective of brain regions for a selected time range, demonstrating time points of when the activity occurs in the slice. (C) Three selected traces: the blue trace from the hippocampal region, the red trace from one end of the neocortex, and the aqua trace from the other end of the neocortex. (D) Zoomed in view of the first seizure [the region bracketed in panel (C) as AA], with the black dashes showing a peak find function within the GUI. (E) This demonstrates the ability to plot filtered traces along with the raw traces. (F) The amplitude frequency transformations for the traces in panels (D,E) (band-pass filtered). The filtered FFT spectrum for each is shown in purple.
Figure 4. Channel groups and raster plot can be generated to visualize LFP activity in different regions of the brain slice. (A) Sensor locations corresponding to three different regions selected for analysis and the region-specific raster plots. Group 1 being the hippocampus, while groups 2 and 3 each being one half of the Neocortex. (B) Summary plots and measures that can be generated within the analysis platform.
Figure 6. Seizure activity tracking over space and time. (A) Seizures in individual channels in a group are automatically detected. Their respective start and end times can be tracked across channels in that group. (B) Regions of the raster between time intervals can be selected as demonstrated to generate seizure maps of selected brain regions within the interval. (C) Seizure map for the time interval selected and channels in the group, including initiation site of the seizure, maximum distance the seizure spread from the initiation point, duration of the seizure, and the rate of seizure spread across the tissue.
Jamstix 4.5.0 Beta 1 (PC) is now available with these changes:BAR EDITOR: copy/paste bars now supports using more than one barBAR EDITOR: copy/paste bars now supports shortcuts Shift+C and Shift+VBAR EDITOR: holding CTRL while clicking the bar editor lock icon will extend the action to all bars of the partPART MENU: added options to lock/unlock all eventsSONG MENU: added global actions to lock/unlock all events in all partsBRAIN: the brain 'Add' menu is now filtered by active brain aspect (groove or accent)BRAIN: added 'Double Bass Logic' to brain 'Add' menuBRAIN: right-clicking on brain background now shows the brain 'Add' menuBRAIN: added menu icon to brain elements to access effector menu via left-click instead of right-click on element nameLIVELOOPS: added MIDI trigger option 'Liveloop Continuous Recompose' to toggle constant part recomposition in liveloop modeLIVELOOPS: added display of liveloop options 'Auto-Advance' and 'Always Recompose' to big time windowTIMELINE: bars with accents now have their bar number underlined in the timelineREVISIONS: loading revisions now uses a file dialog so revisions from any previous project can be loadedREVISIONS: revision files are now named as song name + timestamp for easier recognitionMIDI: auditing the kit in the bar editor or 3D kit with a 3rd party plugin now works properly if the MIDI channel is greater than 1GUI: sliders now support mouse wheel actionsGUI: added option 'Status Line Hint Persistence' to set delay until status bar hint is cleared3D KIT: fixed lights not being recalled correctly on song load
Jamstix 4.4.4 (PC) is now available with these changes:AI: fixed full composition mode ignoring bars when 'BAR' is checkedAI: fixed some songs not playing notes after loading the project even though notes are presentAI: fixed fill end crashes not playing under certain circumstancesAI: fixed global actions fill crash modifiers not affecting some bars under certain circumstancesGUI: fixed RF and TF boxes being 'twitchy' leading to fills sometimes not being in synch with settingGUI: disabled brain elements how have header text in italic with lower opacity and collapseGUI: added song menu option 'Clear'->'Clear Structure Cache' for use with songs that suddenly stop playing even though notes are presentMIDI CC: fixed error when trying to MIDI-map cymbal priority of the kick element in the fill generatorMIDI CC: MIDI controller mapping now has functions to mute drums and Jamcussion (right-click power knob, map 'Muting (Drums)' or 'Muting (Jamcussion)')AUDIO: fixed flanging sounds in groove fills under certain circumstances due to limb check not removing same sounds on both hands on same tickIMPORT: fixed MIDI import preview not working if current bar is beyond length of MIDI file being previewedIMPORT: fixed MIDI importer not setting pedal pressure values for open hihat notes when using mappings that support pressure translationLIVELOOP: fixed recomp/randomize triggers not working correctly in liveloop modeMODELS: default 'Chad' model now uses 0% 'Funk It Up' settingMAPPINGS: added MIDI mappings for Royotoms
Jamstix 4.4.3 is now available with these changes:BRAIN: added 'Stop' capability to fill generator allowing silenced ticks to be used within fillsBRAIN: added 3 new frequency modes for brain effectors (first half, second half, last bar)BRAIN: fixed 'BIAS' knob not updating visually when changed via MIDI controllerBRAIN: fixed 'Priority' knob updating only to -10 or +10 when changed via MIDI controllerGUI: fixed 'U-Pick Metal 2-Bar' being incorrectly attributed to MetalPak instead of AIPakGUI: fixed name of style and drummer preset not being recalled correctly while data itself is fine
Jamstix 4.4.1 is now available with these changes:fixed SSL issue with 4.4.0 under certain circumstancesfixed issues with certain modes in the 'Redirection' elementClick 'Open Manager/Update Tool' in the Jamstix help menu to update. September 4th, 2019NEW RELEASE: \"OddTime\" MiniPakFlexible styles that adapt to any time signature Driven by groove weights for optimal note placementNew drummer model 'Bill'4 new Jamstix stylesSecure Online ShopSeptember 3rd, 2019Jamstix 4.4.0 is now available with these changes:BRAIN: full composition mode now uses multi-threading for less audio artifacts when recomposing large parts on low latency systems (can be toggled via 'Composition Multi-Threading' under 'Options')BRAIN: split style and drummer label in brain for clarityBRAIN: added snare and tom head positioning for MODODRUMBRAIN: fixed brain changes sometimes not triggering recompose in full composition modeBRAIN: fixed brain corruption when violently adjusting knobs or sliders during a part changeBRAIN: fixed brain randomization not working correctly via button or MIDI triggerMAPPINGS: added MIDI mappings for MODODRUMEXPORT: fixed issue with MIDI export when using just the default partEXPORT: fixed issue MIDI exporting last bar of a partGUI: added 'Unlink All Parts' to global action section in the song menuGUI: added 'Recompose Song' to song menuGUI: added options to all three groove weight menus to apply a 2x8th or 3x8th default patternGUI: fixed timeline disappearing in Liveloop mode under certain circumstancesGUI: fixed issue with bar editor display refresh when moving from a song position without part to one with a part while the host is playing3D KIT: fixed environment not fully displaying until kit is pannedJAMMING: fixed jamming options (knobs) not saving changesIMPORT: fixed MIDI importer not reloading time sig when time sig changes for the partPARTS: fixed 'Create New Part' not using source part shuffle settings, weight and timingPARTS: fixed linked parts shuffle settings not being reflected properly in song sheet when loading a shuffled style in the master partSUPPORT: fixed 'Email Tech Support' not including all log files under certain circumstancescompatible with upcoming new MiniPaksClick 'Open Manager/Update Tool' in the Jamstix help menu to update. August 28th, 2019Jamstix 4.4.0 Beta 3 is available. See official 4.4.0 release for details. 59ce067264