Difference between revisions of "The Eyewire Lexicon"
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Smallest unit or resolution in dataset is a [[The_Eyewire_Lexicon#V|voxel]], 16.5 x 16.5 x 23 nm in size. A cube or a volume contain about 256^3 = 1,6777,216 voxels.
Smallest unit or resolution in dataset is a [[The_Eyewire_Lexicon#V|voxel]], 16.5 x 16.5 x 23 nm in size. A cube or a volume contain about 256^3 = 1,6777,216 voxels.
Revision as of 03:10, 18 June 2018
This page holds definitions relevant to Eyewire, as well as terminology created by participants. Feast your eyes and gorge your brain cells on all the knowledge.
Acc/AQC/Accuracy: Player Accuracy is determined after each cube is submitted, it is calculated by the last 60 cubes a player has traced. Level 1 and level 2 accuracies are calculated independently of each other and each has its own bar on the player profile. It is public and can be viewed by looking at a player's profile. Hints for improving accuracy can be found here.
Administrator (Admin): One who works (or has worked) for EyeWire HQ on site. Their roles include but are not limited to: reaping and editing cubes, moderating the chat and forum, presenting new cells for tracing and declaring cells complete, editing the blog and wiki, running in-game competitions and bestowing bonuses upon winners of such competitions. The Admins are also known as "Golden Ones" in reference to the color of their usernames in the chatlog.
AI: Artificial Intelligence. The program AI uses the dark outline of the neuron we just work on in 2D to create the 3D shape. AI is good, but not perfect,,sometimes it fails to fill in all the holes in a neuron, or misses extra nubs and branches in the neuron’s structure. By tracing we players fix the computer program’s mistakes.
Amacrine Cell: A type of neuron in the retina. Bipolar cells make synapses with them, and they make synapses with ganglion cells. There is no true distinction between the dendrites and axon of an amacrine cell. Their projections may be referred to as neurites or Branches for accuracy, or dendrites for simplicity. Starburst Amacrine cells (SAC) are a subtype eyewirers traced in 2013.
Ancestors: Cubes that are closer to the cell body and spawned before a given cube. The immediate ancestor of a cube is it's parent. Scouts/Scythes and Admins can see these cubes (or ID of cubes) by clicking "Show" in the Scout toolbox. These cubes will then be highlighted. See also child.
Artifact Cell: Cells that are playable by all who have completed the initial tutorial. These are the Level 1 cells. The accuracy requirement for trailblazing on these cells is 70%.
Backtrace: A trace going backwards from the point of a merger, allowing one to see that the piece in question is not part of the cell being traced.
Bipolar Cell: A type of neuron in the retina. Photoreceptors and horizontal cells make synapses with them and they make synapses with amacrine and ganglion cells. The name comes from their appearance, as they have one projection on each side of the cell body.
Black spill: (Also called dark spill or ink spill.) A place in the cube where the stain used in the sample has pooled or spread beyond it's target. These places usually look like black spots and rivers. The trace through these areas is often rough, gappy and hard to follow. More info in this video tutorial: https://www.youtube.com/watch?v=Z5K3-z_SM6E
Branch: A synonym for Neurite. Part of the trace in a cube that touches the cube wall and exits (or hits) the end of the dataset. In overview a branch may split, end, or go to the edge of the dataset.
Bouton: The synaptic terminal on the presynaptic cell in a chemical synapse. It contains neurotransmitters that are released when the cell is activated. These also occur along the branches of amacrine and some other cells.
CA: Chat appropriate. Players are expected to keep their language clean and child friendly. This includes topics of conversation as well as the language itself. Type !rules in chat if a reminder is needed.
Cell Body: The large, bulbous part of the neuron, which contains the nucleus and most of the other organelles in a neuron. Type !cb in chat.
Chatstracted: Distracted by CHAT (again, a twisterism)
Child: A cube spawned by the AI when a branch touches the wall between it and another cube (parent). Scouts/Scythes and Admins may click on "show children" when in inspect mode to see any cubes (or a list of their numbers) spawned from their current cube.
Children: All the cubes that have spawned further up the branch from the cube in question (away from the cell body). Scouts/Scythes and Admins may click on "show children" when in inspect mode to see any cubes (or a list of their numbers) spawned from their current cube.
Citizen Science: Citizen science is science that is conducted by the public and often uses amateur scientists to collect and analyze data. Citizen science often relies on crowd sourcing, as is the case with Eyewire. By collecting small amounts of data from a large group of participants, citizen science provides and effective way to expand and improve on current research projects. EyeWire is one of many citizen science projects. Others include Foldit and Zooniverse.
CIW: Chat inappropriate word. See also: ca.
Complete: A function in the Scythe toolbox used when checking a cell to indicate a cube is correct and complete. Two votes indicating "complete" status of a cube will take the cube out of play. In overview the cube will be shown as violet or purple according to whether it has one or two votes. Scythes each have one vote, Admins have 1M votes.
Competitions There are many eyewire competitions. Happy Hours for fun, Marathons will test your endurance, Hunts will push you to the limits of your mental acuity. Evil Cube Challenges and Team challenges will also offer the opportunity to win extra points and even sometimes real swag. When there are open Challenges there will be a blue box on the header bar at the top of the main page where one can choose a team (if relevant to that challenge) or simply register. No registration = no bonuses, so don't forget!
Complete Ancestors: A function in the Scythe toolbox used to mark all the cubes that are direct ancestors of the selected cube complete. Select a cube then hit complete ancestors (or c+down arrow) (first check the branch for completion. Things you mark complete should be perfect)
Complete Children: A function in the Scythe toolbox used to indicate all the cubes that are direct descendants of the selected cube are correct and complete. Select a cube, check the branch for completion, then click complete children (or c+up arrow).
Confidence: The likelihood that a segment belongs to a certain cube, based on how many players have included it in their trace (or on weight added by Scythes and Admins when making corrections). These values may be seen in the cube when a Scout, Scythe or Admin is using the inspect function or from the overview using the Scythe Vision Heat Map. In order of highest to least confidence the colors are (assuming that we use the default colour setting): light blue, dark blue, purple, pink, and orange.
Connectome: A complete wiring diagram of an organism’s neurons. Connectomics is the study of the connectome of an organism. Connectionism is a theory that the neural processes that occur in an organism are dictated by the connections between the neurons. For more information read Dr. Seung's book "Connectome". You can see excerpts from this awesome book here, and you can buy a copy of it here: http://www.amazon.com/Connectome-How-Brains-Wiring-Makes/dp/0547678592.
Consensus: The trace that is accepted to be true for a cube. It changes if other players submit differing traces, and can be deliberately changed by scythes and admins. A weight of no less than 3.0 is required for a consensus to form on mystery cells, and no less than 2.0 for lightning cells.
Cont: Abbreviation for Continue. As in, does this branch cont (extend) or not?
Corner Cubes:: These occur when a trace goes through just a corner of a cube. They usually don't require much added coloring, if any, and still need to be checked. Since they only earn players a small score they don't show up in the chatlog, and may leave new players with the impression that they alone are getting these cubes. Not to worry, the server makes sure we all do our share.
Created:: An option of the "Heat Map" menu. Scouts, Scythes and Admins can select this option to see relative time of creation of cubes. There is also a Slider that changes the sensitivity of this heat map.
Cube: Although our sample is very small physically (only 350x300x60 microns), in the scale at which we are working the dataset is very large. This area has been divided into many smaller spaces which are also called volumes. The size of one of these volumes is 4.1 x4.1 x5.6 microns or 4100x4100x5600 nm. (As you look at your computer screen's resolution, one voxel, the smallest unit, represents an area approximately equal to 16.5x16.5x23 nm. Thus each cube consists of about 256^3 = 1,6777,216 voxels.) Each of these volumes contain sections of dendrites from hundreds of neurons. In order to manage this complexity, players trace one cell at a time as it passes through these spaces. Out of one volume many cubes with individual identification numbers are created, one for each of the different neurons passing through that volume or space in the dataset. As we play Eyewire, our tasks are to follow the traces of each dendrite through each relevant space. These tasks are called cubes. Our cubes overlap each other at their edges so a trace that is close enough to an edge will have an iteration (a trace that is the same) in the next cube. If a trace is near a place where two edges meet it may have as many as 4 iterations, and those near the intersection of three edges of the cube may have as many as eight iterations. This is important to know when correcting a merger or adding a missing part of the trace.
Cubemaster/Cube Mistress: Someone who is sitting on a cell, single-mindedly working towards its completion.
2D/3D: The 2D image is a cross section or a slice of the 3D. Think of a stack of 2D images in the 3D-cube like in a flip book. Scrolling through the slices one can follow the shape of a neuron and color segments of this neuron AI missed. Colorings in 2D will be immediately transcribed into 3D, the 3-dimensional image of the traced neuron.
Dataset: Dataset E2198 was taken from a mouse-retina with a Scanning Electron Microscope (mouse unofficially called Harold), at Max Planck Institute, Germany. Size of the dataset is 350x300x60 microns.
Debug: Typing /debug in the chat box will bring up information about the location of one's cursor in the dataset if in overview, or information in a selected cube including the cell number, the coordinates of the center of the cell, the cube ID, the presenting axis (xy, xz,or yz), and the ID of the last segment traced. This information is present both in overview and from within a cube. To remove this information from the screen, type /debug again.
Dendrite: A projection from the cell body that receives electrochemical signals from other cells through synapses and carries them to the Cell Body. In amacrine cells which have no axon these projections are simply called neurites.
Deja-Cube: A term used to describe that feeling that you've done the same cube (or trace) before. It may be triggered by a cube that overlaps one you did before that has part(s) of the same seed and trace. Coined by player Faunhaert.
Downstream: Cubes which are closer to the cell body than the selected cube.
Dread 20/40: A situation in which a cube that should have been worth a lot more than 20/40pts, only yielded 20/40pts. Dread 20/40 may have been caused by Trailblazer or 2nd person error. If the Trailblazer missed a fair amount of volume, you could have points deducted from your score for "overtracing" (coloring in areas that are not part of the neuritebeing followed). Take a screen shot and alert a Scythe or Admin. If the cube is then reaped, your accuracy will be restored. Note that Dread 20 and Dread 40 are the most common amount of points given in these situations (20 or 40 being maximum time points for level 1/level 2), but other values are possible. Coined by player mam711.
Duplicate Cube/Dupe: A term used by Scouts, Scythes, and Admins which indicates a cube which contains a segments or multiple segments from another cell. It is seen as a blue color in Scythe Vision.
Dust: One or more small segments that have been missed by the AI when spawning the cube, or by players when tracing it. (In contrast to a nub which projects from the dendrite and changes the profile of the trace.)
EOS Cube: End of sample/edge of sample cube, a cube which is on the edge of the examined sample, often contains multiple misalignments. Coined by player skruffylooter.
Explore Mode: A feature that allows a player to trace in a third color, different from that of their trace and the seed. The player can then can choose to include or omit the “explored” segments from their final trace. This feature is especially helpful when using a process of elimination to follow a difficult trace.
Flag: A tool in the scout toolbox used by scouts to draw attention to a certain cube when using Scythe Vision in overview. Causes the cube to show up as yellow. inspect a cube and click "flag".
Flaglog: Verb meaning to flag + log a cube. In fact, a scout should never just flag. They should Flaglog. Coined by player Cliodhna.
Flipping the cube/Changing Planes: Rotating the cube 90 degrees so the 2D plane lies on another axis. This can be done by Alt+(L)click+drag in the 2d screen. Useful for checking traces. To check which plane you are in type /debug in chat. To clear this information from your screen type /debug again.
Fort Scythe: A cell which is only to be ReapGrown by scythes, and scythe completed after.
Gamemaster: Another term for an admin (in eyewire) who is in charge of the game-play.
Ganglion Cell: The neurons responsible for transferring information from the retina to the brain.
Glial Cell: The cells that support and protect neurons. They hold the neurons in place, supply them nutrients and oxygen, insulate them from one another, destroy pathogens and remove dead neurons. In the cubes, they show up as amorphous, huge blobs.
Glial goo: The evilness of glial when it latches onto something else that is legit.
Golden One(s): A term for admins/devs. Refers to the gold color they use in chat.
GrimReaper: An all powerful being in EyeWire. Has the abilities to remove mergers, extend branches, assign duplicate cubes to the correct cell, give points to those who lend a hand, and take points away from those who work to hinder scientific progress.
Harold: The unofficial name of the mouse who donated his retina to science! Harold's retina was harvested and converted to data long before Eyewire began.
HH, Happy Hour: An event held on Thursdays from the hours of 8 am to 10 am EST and on Fridays from the hours of 2-4 pm EST where bonus points are awarded for a certain number of points traced (starting at 2500). On special occasions Admins may also hold spontaneous Happy Hours. See schedules here.
Heat Map: A function in EyeWire used by Scouts, Scythes, and Admins to visualize information about the cell, using each cube as a single data point.
Hunt: A challenge in which a cell is chosen and mergers are added to it. Players must find and report all mergers in order to win.
Inspect: Term that Scouts, Scythes and admins use to signify entering a cube from overview or after jumping from a cube given in chat. A function present in the scout's toolbox.
JAM-B (J) Cell: A subcategory of direction-selective ganglion cells that have an asymmetric dendritic arbor. In other words, the dendrite branches are not evenly distributed in the space around the cell body.
Jump (In Cube): A term Scouts, Scythes and admins use to jump to a child or parent cube of the currently selected cube, or from an ID given in chat.
Last Scythe Wins (LSW): Last scythe to reap a cube sets the consensus, regardless of weight. More information here: http://blog.eyewire.org/last-scythe-wins
Lightning Cell: The old name of Relic cells. Cell ranking was instituted after the end of the Starburst Challenge. See alsoː Relic Cell.
Lightning Tutorial: A series of cubes picked to train players to deal with the potential problems they will run into in Lightning cells.
Low Conf, Low Confidence: A trace (or segments) in a cube that are pink/red in color when seen in inspect. Such a cube needs more traces containing those pieces, or to be locked.
Magic Mode: Magic Mode is an experimental feature that allows you to interact directly in 3D. Simply click any point on the branch in your cube to add the segment directly adjacent to it.
Marathon: A challenge in which all players have to work together with admins, to try to complete a cell in under 24 hours.
Mentor: An advanced player role enabling one to join other players in their cube in order to help them overcome a difficulty or teach them how to play. Requesting a mentor must be done in public chat or in scout chat if made by one scout to another. Mentors will appear in the chat with Hello-Kitty pink username. See blog post.
Merger: An error in the reconstruction of the cell in which a part of another cell has been mistakenly included in the cell in question. This could be caused by faulty segmentation, a problem in the seed of a cube, artifacts in the image data, mistakes by the players, or a combination of any of the reasons. http://wiki.eyewire.org/en/Mergers. Type !merger in chat.
Misalignment: An artifact in the data in which the slides appear to shift over. The shift might be sudden or there may be a white slide in between the two sides of the misalignment. They are more common close to the edge of the dataset.
Moderator: Players who have assumed the responsibility of being caretakers of our eyewire culture in chat. Among their duties are welcoming new and returning players, keeping the language and topics of conversation child-friendly and encouraging players by example to interact in a constructive manner. They may remind players of the rules of chat. Their tools include the ability to mute players who continue to break the rules. Moderators will appear in chat with glowing purple username.
Mootstashed: An adjective describing a cube that had an issue requiring scout/scythe/admin attention, but got stashed, rendering the issue moot.
Mystery Cell: Old name of Artifact Cells. See alsoː Artifact Cell
Nub: A projection off the branch of a neuron that is short and may serve to form a synapse.
Nublets: Little tiny baby nubs. Usually used when there are a lot of them in a cube.
OMCS: One More Cube Syndrome - when player cannot stop, must trace just one more cube. Coined by player Nseraf. If working in the wiki, it may also refer to "One more correction syndrome".
Omni: Omni is Eyewire's big brother. It is used by expert tracers in the lab. Omni uses larger data sets than Eyewire to render 3D images of neurons, but otherwise they are very similar, and drive towards the same goals.
Orientation: Each cube has 3 axes x,y,z and 3 orientations of planes; xy, xz and yz.To change orientation use alt + drag with mouse on 2d. This is very useful for finding extensions. In case of the misalignments xy-plane is the best to find correct trace (xy-plane is the one the original slices are seated).
Overcoloring: A calculation of the percentage of the total incorrect volume added to the trace.
Overview: The 3D representation of whole cells in EyeWire.
Parent: A cube in which a branch (or branches) touch the wall spawning another cube - used to check traces in child.
Playcomplete: Play a cube, exit to overview to check it, scythe complete it, then return to submit it. Useful for finding little errors when a cell is nearing completion.
Player Roles: Players have different roles according to their level of experience, expertise, and interests. See http://wiki.eyewire.org/en/Player_Roles
PM Me: "Please send a private message to me" containing whatever topic of discussion.
Poof: Exclamation used to express that a merger has disappeared from overview after reaping a cube it started in. Possibly coined by Nseraf.
Power Tra(cing/er): Combining very high accuracy (95%+) with high submition speed. In theory a power tracer can accumulate 10.000 points per hour every hour if a Lv 2 cell is available. Taking advantage of his/her speed with great accuracy one can squeeze out the max. amount of points each cube has to give. Coined by player Nseraf.
Reap: To re-weigh the consensus of the currently selected cube. This can be done by Scythes and Admins. Re-reaping a cube (a second time) after having added or removed one more more segments reallocates each scythe's 2 reap weight to the new trace. Depending on the weight of the cube it may take more than one scythe to add or remove something from the consensus. Unless the cube is marked "complete" players can still play that cube which may result in loss of the correction. An admin reaps with a weight of 1 million making further changes by others impossible. Reaping a cube will turn it orange if reaped by a scythe (unless it was previously scouted, in which case it remains yellow) or red if reaped by an admin. To reap a cube, enter it with the inspect tool, make necessary changes to correct the trace, and then click the button "reap".
Reapgrow: With direction or permission from Admins, scythes/admins reap traces without logging just to grow a branch/cell. Usually done to complete an errand branch in an otherwise finished cell or in special HQ missions when they find missing branches in previously completed cells.
Reapviewː When an admin reviews+reaps a cell to complete it. reap+review= reapview. Another twisterism.
Relic Cellː Level 2 cells, these are more difficult than Level 1 (Artifact) cells. Points earned on these cells are doubled. The accuracy requirement for trailblazing on these cells is 80%.
Requestractions: those REQUESTS that are DISTRACTIONS from the work at hand (coined by twister2).
Resolution: Smallest unit or resolution in dataset is a voxel, 16.5 x 16.5 x 23 nm in size. A cube or a volume contain about 256^3 = 1,6777,216 voxels.
<!-T:112--> Retrocascade: The waterfall of retroactive trailblaze points messages that floods the chat when the spawner is restarted after being down for a significant period of time. (coined by twister2)
SBEM: Serial Block Electron Microscopy or Serial Block Face Electron Microscopy (SBFSEM) was specifically developed for imaging neurons. After the sample is stained with a heavy metal, it is inserted into the SEM. The surface of the sample is imaged and then it is shaved off, exposing a layer of the surface underneath the layer that was just imaged. While this is a very effective process, it is also destructive to the sample; if a mistake is made, there is no second chance. Misalignments are the expression of such faults.
Scout: A player who looks for mergers, missing branches, and missing nubs in the reconstruction of cells. The colour of scouts is turquoise.
SC: Scythe complete. When a Scythe or Admin marks a cube as 'complete' in overview. Requires two scythes or one Admin to 'lock' so the cube is no longer in play. This status may be seen using the weight Heat Map. Scing is the verb form. Coined by Nseraf.
Scythe: An advanced player who works with other Scouts and Scythes to correct mergers, and/or to add missing branches and nubs in the reconstruction of cells. The colour of scythes is glowing turquoise.
Scing: The verb form of "sc" (scythe complete).
Scything: The act of reaping a cube (by a scythe).
Seed: The initial segments that are given to a player when entering a cube. These segments are present in the overlap from the parent cube and are presented as the beginning of the trace in the child. In default color mode the Seed is blue.
Segment: Subdivisions of the data which an artificial intelligence has decided belong together. Players must chose all the segments belonging to the neuron when tracing a cube and avoid coloring those which do not belong.
Slurking: Slithering+lurking (created by twister2, applied sometimes to him).
Snapper: A cube wherein you get a Dread 20/40, but when you inspect it, the trace is already correct (i.e. your trace snapped the consensus; you are the tiebreaker). Coined by player mam711.
Soma: A synonym for Cell Body.
Squigglebranch: A branch that moves like a snake back and forth across the cube. Coined by player Andrearwen.
Starburst Amacrine Cell: A type of Amacrine cell that plays a role in directional selectivity. Starburst amacrine cells (SAC) are a subtype of retinal amacrine cells traced by eyewirers in 2013. Their dendritic arbor has a characteristic “starburst” shape. Two main roles for starburst amacrine cell have been characterized. SACs are (1) important in the computation of direction-selectivity and they also serve (2) an important function in the development of the retina. 29 starburst neurons reconstructed by eyewirers (starburst challenge) were used for a publication in nature: “Space–time wiring specificity supports direction selectivity in the retina” (Jinseop et al, may 2014). [http://blog.eyewire.org/eyewires-first-scientific-discovery-and-nature-paper/ ]
Starburst Challenge: A challenge in EyeWire where players were mapping as many Starburst Amacrine Cells as possible. This challenge has since been completed.
Stashed: A cube that has been removed by a Scythe or Admin (or is lost when a trace changes or eliminates the parent cube) from the cell. This cube status can be seen if you scroll down in the scout toolbox.
Synapse: A connection between the axon of one cell and the dendrite of another. In chemical synapses, neurotransmitters are released from the presynaptic cell’s axon and are absorbed by the postsynaptic cell’s dendrite. In electrical synapses, an action potential flows directly from the axon of one cell to the dendrite of another through a shared cytoplasm.
Task: A synonym for cube.
Trace: The segments in a cube that a player colors in and submits.
Trailblazing/er: Being the first person to trace a cube. A player must have 80% accuracy to be eligible. For further explanation, type !tb in chat.
Trainee: A beginning player who is working on the basic tutorial and has no access to other cubes.
Undercoloring: A calculation of the percentage of total volume missing from a player’s trace.
Upstream: Cubes which are farther away from the cell body than the selected cube.
Volume: The units into which the 3D image of the whole sample is divided are the volumes, and each volume overlaps with its neighbors. The size of one of these volumes is 4.1 x4.1 x5.6 microns or 4100x4100x5600 nm. (As you look at your computer screen's resolution, one voxel, the smallest unit, represents an area approximately equal to 16.5x16.5x23 nm.) Each of these volumes contain sections of dendrites from hundreds of neurons. In order to manage this complexity, players trace one cell at a time as it passes through these spaces. Out of one volume many cubes with individual identification numbers are created, one for each of the different neurons passing through that volume or space in the dataset.
Voxel: The abbreviation of 'volume pixel', the 3D equivalent of a pixel.
Wall Crawling: Coloring in a low profile trace that follows along a wall. Coined by player Jwb52z.
Wall Trace: Low profile traces that follow along a wall (often missed by players).
(Please) watch me: Requesting a mentor come into the cube to assist per "mentor rules". The request must be made in general chat, or in scout chat if made by one scout to another.
Watchtrace: Mentoring in order to trace a cube for someone. Done only as a teaching strategy . Coined by player mam711.
Weight: The total amount of validations made on a cube.. An unenfranchised player has a weight of 0.1 and a regular player has a weight of one. A scythe has a weight of two. When reaping a cube, an Admin has a weight of one million. Relative weights of the cubes in a cell may be seen by Scouts, Scythes and Admins on the weight heat map.
Zombie Merger: A merger that "comes back from the dead" after being reaped out, usually because it was later traced in an overlapping cube, or because it was already in an overlapping cube but the reaper(s) only removed it from the first cube, forgetting to make sure the merger was gone from all the cube's iterations. (coined by Atani)
Zemo: The (un)official name of the zebrafish whose sample mystics and princeton tracers are reconstructing neurons in, in 2017. (coined by mystic dragonturtle).