RZ10x Initial Training
We're going to go over the hardware setup software setup and all that kind of stuff which is great and talk about you know RZ10x in the context of photometry maybe the differences I don't know if you've ever used our RZ5P system but at the end there um is this manual which is basically going to go over ever you know goes over everything that I want to talk about today actually in more detail but of course it's easier to learn when you're you know communicating with somebody but you know once you have that context you can go back and check out this manual and it'll walk you through everything in case you forget anything you can of course email me with questions but the manual is pretty comprehensive all right so first things first we have the RZ10x it's on so i'm going to go to zBusMon and then i'm going to press this transfer test and that's going to basically just tell me whether or not i'm communicating properly with the system. Anytime you update the drivers or anything on the RZ10x you'll have to update the microcode in zBusMon which is this v95 thing down here right now it's white because it is matching the driver code if it wasn't it'd be red um so there's instructions online for all that kind of stuff but i just start there all right now we'll head over to synapse all right so here's synapse if i go to menu edit rig here's where my hardware shows up we have the RZ10x three DSPs that's all well and good the DSPs are the basically the processing cards inside the RZ10x so there's nothing to do here the only thing you would end up doing is if you wanted to add a camera like a USB camera for example you would right click here and say add cam and then you can add a USB camera that way pretty straightforward now in the space Synapse menu all right we have no experiment or subject setup um and okay i guess this is a fresh computer entirely so basically what we'll want to do is make a new experiment uh and a new subject because right now we can't record anything because we don't have either of those defined so if i click on the experiment name i'll just say new and we'll just call it setup and now I'll make a new subject all right so now i have a subject and an experiment name and now this record button is available to me now why is that the case well the way that the data is saved and we'll get to this later but the way the data saved is basically there's this folder of tanks and then inside the tanks are these individual blocks which are your recordings and inside the blocks are individual files that you know make up the block and we'll see this later but anyways the way it's structured is that the the tank inherits the you know experiment name and then each recording ex inherits the the subject name and then the date it was created and this will make more sense once we see some recordings but that's just a little context as to why the record button was gone before we you know if i make any of these blank the record button goes away okay so what we've seen the processing tree first is this rc10x this is of course our main processor um and what we want to do is just go through the tabs and understand them so on this main tab for photometry unless you're doing like efiz or something else this device rate can stay at 6k for photometry 6 kilohertz is plenty i mean you're generating up to maybe a 500 hertz sine wave modulation for modulating these leds so sampling it at 6k is going to give you a nice clean sine wave so you're good there if you wanted to generate tones or record something beyond like three kilohertz in terms of frequency content then you'd have to bump that up uh you don't need to probably touch the load optimization if you do then i'd be involved um this tick store uh is basically just a one second tick mark on your plot you can have it on you can have it off it doesn't really matter um that doesn't do too much uh the important thing on this page probably is this runtime notes so if i click notes plus epochs basically you can make some comma delimited notes like air puff injection uh tail pinch food drop etc um and basically during record mode there'll be preset buttons that you can punch and then it'll time stamp when that happened with the associated note file and code so if you're doing some you know in vivo testing and it's not sort of well time locked to some sort of behavioral event or something and you're just doing air puffs and you want to do some sort of trial event based averaging then you can use these runtime notes to do that um so you can see when i made a change this commit button showed up anytime you make a change in synapse you press commit and that's gonna basically in this revision log track all the changes that you've ever made so it starts at 17 whatever sometimes it starts at random numbers but in any case you can see here i added some record notes okay if you wanted to go back in time ever you can revert back to an old version of the experiment i'll click on here there's no runtime notes and then let's say oops i didn't want to do that i go back to this other edit that i did and now they're back there's a database underneath that controls all of that for the rz10x what you want to do is once you're plugged in and communicated you want to go to this lux tab and press detect hardware what this is going to do is it's going to ping the rz10x and you know basically figure out what leds what sensors you have connected so what do we have connected here we have a 405 465 for your iso specific control and for your calcium signal or whatever delay whatever over here driver three is empty so it has an m8 connector and any connectors connecting from you know the rc10x to an external led would be the traditional way of doing it the sensor a and the sensor c both have photo sensors in them ps1 photo sensors and then send b here has a b and c and send d has a pm1 so this pm wants a power meter and you can basically access that from the top bank or the lower bank however traditionally when you add a photometric gizmo which we'll see in a second each row talks to only one photometry gizmo so the only special device that talks across gizmos is this pm1 and then this bnc here is can be accessed as an input if you have some sort of random signal coming in otherwise you just leave it alone if you ever make a change so for example if you swap leds add an led add a photo sensor what have you uh you'd have to re-detect the hardware now the cool thing is and we'll see in a second once i add a photography gizmo it's going to automatically recognize what i have in each row going to this digital i o so this is important in photometry for a lot of people this digital i o is going to be your input output for external devices that send ttl communications behavioral codes very common thing is maybe med associates harvard apparatus lafayette something like that where you hook up maybe like a db25 cable to the front db25 port of the rz10x you'll see there's a gb25 connector and it says digital i o there's also four bncs labeled zero one two and three so the db25 connector talks to all 24 of these bits the front b and c's are mapped to these four individual bits right here which are bit addressable so you can capture individual ttls typically with met associates you'll enable port a at the very least and then you can either group port c as a single port or have them all bit addressable but let's just worry about port a right now you enable it permit associates they go from five to zero when something happens so you typically want to invert it because it's easier to think of it as going from low to high and then you just add this epoch store here and then it'll capture the bit code coming in so what's a bit code well port a monitors all eight bits at once so if i jump here really quickly and go to tdt.com hardware manuals processors rz10x on this digital i o here what you'll see is um port a is over here in um pin 6 you know 6 19 you know this section right here is port a and basically what happens is all eight of these bits are monitored at once so when you have an input coming in let's say met associates which is hooked up via a cable here and here you know let's say a lever gets pressed and then met associates is one one one you know zero one one one one right so you have bits 0 1 2 3 4 5 6 7 and then when the lever press happened you know bit 4 over here gets flipped from a 1 to a 0. what's going to happen is well technically i inverted everything so the way it would look is zero zero zero one zero zero zero zero and what you would get reported is in synapse you'd see a zero and then when the lever press happened a uh let's see this is two to the zero so that's let's see one two four eight sixteen you get a value of 16 coming through so when that lever press happened you get a 16 and then when turned off you get a zero does that make sense yep it'll make a lot more sense too once it's contextualized but in any case that's sort of what the port a is doing now these port c's over here are bit addressable which means you can monitor individual bits instead of the whole byte at once so when you get something coming in you'll get the onset and the offset and the way you would enable that is boom and then maybe consider inverting it depending on what the signal is if it's for med associates you almost always invert it and then you press commit and then that makes a change and it captures it and that's all you have to do there most of the time for photometry especially on the rz10x you're not going to access these these are analog input analog output that's a little bit about the rz10x the next step is to add the photometry gizmo to the bank we want to talk to in this case we'll just target the upper bank but we're going to press specialized so this tree over here is the gizmo tree and it basically has some of your gizmos that you have available to you not all of them because synapse actually will prune this list based on available input and output connections but here's our photometry gizmo one little neat thing here is if you're ever curious about a gizmo you can click this question mark here and then click on a gizmo and then it brings up a little bit like a little slideshow telling you a little bit more about that gizmo and typical input out can put connections but in any case this photometry so we're going to double click here it's going to tie itself to the rz10x you for the most part want it always tied to this enable line which means it'll be active this green thing is a logic signal so this enable line is a special line on the rz10x you'll see here that there are a couple of different um available connections for photometry most of the time you want it tied to enable but these different connections enable is something where when you start the recording it's a logic signal that just goes high and stays high reset is a once sample logic signal that pulses at the very start of your recording sweep fire something that ticks every one second so you get a logic pulse every one second and then these are your digital inputs and those are the only available connections to you because this requires a logic input and those are the only logic signals available so that's that now the difference between this blue and green here by the way this green is logic this is a floating point signal this is sort of getting into the weeds a little bit but that's a little bit about what this picture is and why it matters uh in any case this auto connects to the um to the upper bank for you and then if you're at a second photometer gizmo double click here it'll tie itself to the lower bank so for the most part you don't need to worry about it but for the keenly observant here you'll see that the difference here is look at how many logic things i have here and i have like one here and for the photometry it goes away depending on what i click on so synapse is pruning that whole list for you in any case let me delete the second photometer gizmo go back here all right so we have our drivers connected here we don't have a third driver so we can disable that but we have this 405 and the 465 so those are our leds that auto populates the name there this max current most of the time you'll have it set to 200 that's just the maximum driving current for that led if you have to go higher then we can bump that up but for photometry probably 200 it's going to be okay these frequencies down here are your demodulation frequencies so for lock and amplification the way that it works is you modulate these leds and these leds are running simultaneously and you're sending light of different wavelengths down the same fiber so what we need to do is we need to modulate them because on our photo sensor when the light comes back out so you know we send light down stuff happens in the brain light comes back out to a photo sensor the photo sensor sends a signal to the rz10x well we need to pick out exactly what's changing in the 405 and 465 return signals and the way we do that is we pick up sort of the frequency content on the return signal so the photo sensor has 210 hertz 330 hertz 60hz 120hz a bunch of garbage on it too and basically we pick out through this thing called lock and amplification uh how much of 210 hertz or how much of 330 hertz is on that return signal and then you can and then you can monitor how much is the amplitude of that signal is changing so that's why we're driving these at different frequencies and you can change that too you know you can make these driver frequencies different as long as they're not multiples of each other or multiples of 60 hertz the reason why you don't do multiple 60 hertz is because that's what your wall power is at this level here is the peak to peak level of your driver led modulation so typically when you need to change the power of your led and we'll talk about power later you'll be changing a level and then the offset here should probably never drop below five uh for these leds you know they're modulating like this but they have a um a dc offset that's needed in order to stay on what happens is that the dc offsets too low then the led might turn off for part of its modulation cycle which would break the lock and amplification so that's important there as a matter of fact you just click this auto calculate offsets and never have to really worry about that because it'll just set it for you um so that's a little bit about that the um launch power estimate i never i never use that it'll basically try and estimate the transmission percent loss in your optical chain so here are our sensors we only have one photo sensor so you know it populates a and b one of them is a b and c if you wanted to for example use an external photo sensor you could do that but in general the is in the sene position and then you can have this checked here the clip threshold we know for the ps1 that it's 9.5 so you don't need to calibrate the clip threshold at all if you had an external photo sensor you would be changing the clip threshold based on you know when it saturates which we can you know go over if that's ever the case um the important thing here besides just activating the correct one is this filter order i would say six is a good filter order that's just the steepness of a low-pass filter that's on the demodulated signal and then the default low pass is at six hertz which is pretty much good for most i would say most uh sensors they're getting a little faster so maybe you can always bump this up to 10 or something like that but in general you know gephi's are really slow so six hertz should be able to finally capture all of your signal it's a low pass filter on your demodulated signal so you know gcam 6 you know has a rising time of like a couple hundred milliseconds so having a low pass filter at six search is totally fine gcamp 8f might be a little bit faster so maybe you bump this up to get a higher resolution the lower this is the smoother your signal is but that'll also you know attenuate content beyond for example two hertz three or four hertz depending on what the corner frequency is so six is fine if anything go up don't go down this demodulators tab is going to control a couple things if you had a second light over here this driver 3 would be active and the sensor b would be active and you would set up the table appropriately to say all right i want to demodulate my 405 signal with the signal on sensor a my 465 on the sensor a signal that's that locking amplification i told you about and then if you had a second sensor here at 560 that would be picked up on a an additional sensor b so you'd say only demodulate 560 with my sensor b but you only have two lights right now one photo sensor so the default table totally fine calculated outputs if you wanted to do some sort of like online normalization it's not really a delta f over f you would publish with but you could do this dff here and even subtract it with the dff of another signal and it's doing the dff by making the f naught the mean of a moving five second window it's soon you know all that's gonna do is normalize your signal for you it's gonna look very similar to the demodulated signal as is so you can have it you can not have it doesn't matter in these lux options you have this thing called timing control um what basically that is is it is a sort of a pulse generator for if you're doing longer recordings you can turn the leds on for a set period of time turn them off for a set period of time and do that for a set number of repeats so people who record more than maybe one to two hours aren't gonna be using this because you don't want to bleach your um guffy and so you know you turn the leds off after like 30 minutes and then turn them on 30 minutes later something like that so that's what these timing controls do this target range right here is going to control when you do power measurements there's a little bar graph and it's just a visual indicator i just leave it at 10. it doesn't control
anything it's just a dummy indicator and then this assigned lux io bank it's tied to the upper bank i don't see typically a reason why to change that over here in this miscellaneous you can store the driver signals or not uh there's really no reason unless you're doing your own demodulation and so you know that's all that that does here the only special thing about this tab is if you want your drivers on immediately when you start runtime you can click this button and it will do that so that's the photometry gizmo now i guess the next step is to talk about the physical connections um from the rz10x to the mini cube to the photo sensors and subject so the most important thing um is making sure that you have the right cables in the right spots and that the cables are connected properly so these cables if i go back here photometry guide let's go to the getting started these cables have a little notch and key mechanism and you have to make sure that those are aligned so there's a little metal bump on these fc this is called an fcm connector and then this is the fc connector they have a little bump here and a little notch here and then they have to be aligned so in the tpt lux cable kit you're going to connect the 200 micron cables from the 405 465 see the appropriate input ports maybe the ie and e1 ports respectively of the mini cube if you have your own cables that's fine too um but if you have the lux cable kit those are to connect there and then the subject cables the subject cable um in the lux cable kit there is a 400 micron cable that can serve as a pseudo subject cable which we'll get to in a second when we do power measurements and then you have a 600 micron cable that will go from your f1 port which is the fluorescent output port to your ps1 in sensor a let's just go to preview so first things first let me auto scale and then i'm going to right click this five foe tab and split that over to the right whoops missed that let's merge down right click split right so what i'm seeing over here is these are my that's my note epoch you can see my runtime recording notes only available during record mode but here are the preset buttons uh these that's my port a input for the digital i o these are bits c0 c1 if you activate all the bits of course you'd see more this is my demodulated 405 signal this is my deep modulated 465 signal now there's nothing happening right now but you're going to get this is what we call lock and amplification or demodulation noise basically you know it's gonna not be non-zero because you have this noisy photo sensor here and i'm sure there's a little bit of 210 hertz and a little bit of 330 hertz on the signal even if it's a tiny bit but once we turn the lights on you'll see that this jumps you know should jump way up depending on how bright the signal is or what you're connected to you see this jump way up now you can auto scale or you can hold shift and drag like this and then hold ctrl and drag like this now it wasn't much of a jump probably because we're not pointed at anything fluorescent in particular but we'll get to that in a second so auto scale yeah autoscale sometimes fails to do a good job and so i like to hold shift and drag like that in any case this is our raw photo sensor signal here you can see it picked up a little bit of the dc shift when i turn the light on and off like this boom and then boom so that's pretty straightforward um of course here's where i control whether lights turn on and off here's the corner frequency for that low pass filter i talked about here's where i change the peak to peak level which we'll see once we hook up the power meter we'll control the overall power now you can't say oh 10 milliamps equals 10 microwatts you know it all depends empirically on the optical chain and each optical chain is going to be different so what we want to do first and foremost is just get an idea roughly of the power that we're me using at the tip of our fiber so in the luxe cable kit there should be a 400 micron fcfc pseudo subject cable which you can hook up to your sample port of the mini cube and then plug the other end into the pm1 which is on your sensor d of the rz10x this is just going to give us an idea roughly what the power is now this is only valid if your subject cables are the same core diameter as the cable that you use to estimate the power so in the case of the cable we gave you it's 400 microns your subject cables would have to have a 400 micron core diameter otherwise not going to be a great estimate this is going to be for estimating the power um you know giving giving you a bar ballpark are my lights working how much power is coming out of this fiber tip and then your subject cable is going to be very similar the issue with the pm1 is there's not a good way to stick that mf connector on your actual subject cable into the pm1 and get a good estimate because it depends on the depth and stuff like that now i know your group has external power meters so you can use those as well we're working on adapters for the uh mf cable in any case all right so we hooked up the um fcfc connector from the sample port of the mini cube to the ps1 sorry pm1 i'm going to turn these lights on all right something's not correct here so let's check to make sure that we connected from the sample port to the pm1 which is on cnd now the reason why i knew something was wrong is because the pm1 has fluorescent slides in them so when i turned on the leds it didn't jump up crazy like it did just now which you would expect so again holding shift dragging you can see here really really jumps up or i can auto scale like that and then it'll you know hit where i'm looking for now one thing that's important to note is all right so when we're doing this you know pm1 testing i need to activate this power meter right here but the first thing you'll see is that these numbers over here jump up this is your ps1 photo sensor most of the time this is what you care about but when you're doing power meter testing you click this parameter here and the only thing you care about is actually the pm1 bar because what can happen is you can actually end up clipping the ps1 photo sensor so you want to just ignore the quality factor and the values coming out here we'll talk about these later when we're actually doing fluorescent testing one thing to note here is that um these these values that you see here uh in the you know this 1730 and stuff like that those correspond to the amplitudes that you're seeing over here and then the values over here in the pm1 again i'd click this power meter button here toggle that on and off only available in preview mode um the the values you care about right now are these power measurements in microwatts right over here so again we just so happen to be lucky that we're not clipping but if i were to bump this up for example to like 50 you'll see here we start to clip we're saturating the photo sensor you'll see this quality factor drop so some people look at that and say oh bad but no because we're you know we're in the ps1 sorry pm1 so we don't care about the ps1 bar graph right now in any case let me go back down to 10. all right so looking at the right side bar what do we see we have this yellow green red remember that power target range of 10 microwatts i talked about earlier that's what this green thing is it doesn't mean anything it's arbitrary all that you care about really is this number that you're seeing here so for photometry uh it really depends on what you're using but typically i recommend 10 to 30 microwatts is a good starting point for most things d light maybe a little bit on the higher end 30 is good gcamp 10 10 to 20 to 30 is totally fine so what you'll see here is you know you change the the power over here and then the level sorry you change the level and then the power goes up so for example 25 is a fine starting point let's um let's start there and we'll say okay 21 milliamp peak to peak modulation on my 465 led is about 25 microwatts measured through this particular cable unless you have issues with the actual subject cable it should be pretty good ballpark estimate uh that you're running about 25 you should use your external power meter um to verify though uh in any case all right we can turn this one on it doesn't they can both be on by the way um so i don't know why i turn that off old habit because i was talking about external power meters which you have to run one light at a time um so the 405 and the this is typical it's going to run a little bit colder than the uh than the four six five that being said uh you probably don't even need to run the 405 as hot as the four six five because all it needs to do is pick up bleaching if it's there and motion artifact if it's there and this is something that you'll sort of get a better grip on once you're actually doing an in vivo recording you'll see some signal maybe on the 465 and if you don't see anything on the 405 let's say it's flat-ish maybe bump up the 405 and try and figure out whether you're actually seeing a real signal or whether it's motion artifact that's something that once you have an animal it'll make a lot more sense it's hard to visualize if you've never seen it before though just you know talking about it in the abstract in any case 20 and 25 that sounds pretty good so i'm happy with those levels we can turn those off and once we're done with the power meter we just toggle that off one thing i want to talk about real quick is this q factor this quality factor what that's measuring is basically the amount of return fluorescence that you're seeing at that particular driver frequency so with the q factor of 99 what you're seeing is really nice clean um 330 hertz signal and that the signal to noise so the background noise is a certain amount and then the 330 hertz content on that signal is you know much much much higher than the background noise so what you get is this high uh high signal to noise on on the so it's always going to be q factor here but here you can toggle this between q and signal to noise over here i just leave it as q factor um it's really a distortion metric so if the q factor is low that means you have a distorted you know 330 hertz or 210 hertz and you'll see that yes that is the case over here because since we're clipping on the top end your signal actually looks like this and so you're not picking up 330 hertz because that's not 330 hertz because it's flat at the top or if you have such a low signal and this happens sometimes if you have such a low signal that relative to the background noise it ain't much so that happens a lot when you're inside of the animal and for example let's go to this troubleshooting page can't get a response a lot of the time if there's an air gap in between the tip of your fiber and the top of your optical implant air is the worst enemy of your signal because it'll attenuate it so if there's an air gap that's a big problem so a lot of the time when you plug in an animal the q factor might be 92 93 percent um and then what that means is that you're not picking up a very bright return signal because the background noise and the signal you care about at 210 330 or whatever are comparable um in any case okay the other thing that we see here is fiber bleaching the default here actually should be set to i would say four hours would be the minimum um i'm sorry the maximum that i would do and typically you know for fiber bleaching probably get away with doing one hour one to two hours a week but basically what is fiber bleaching well you know these cables aren't perfect so they have these you know they have autofluorescence on them uh and what fiber bleaching does is you're gonna hook up the subject cable in particular you don't really need to hook up the other cables but take the subject cable hook it up directly to your 465 led run this fiber bleaching for one to two hours one hour should be fine because it's an exponential process so you blast a bunch of light through it obviously making sure that the cable is not anywhere where someone can accidentally be staring at it um and what happens is you know the amount of autofluorescence on this cable is gonna reduce by like 80 percent in the first hour and then you know another additional 10 percent would be another hour another additional two percent would be another hour so it really falls off um and then the autofluorescence in the cable recovers at a much slower time scale on scale of days to weeks so if you photobleach your cable like once a week you should be pretty good to go the official recommendations to do it every day but that's a bit excessive in any case um what you do is again hook that the fiber directly up to the led the 465 led and you'll turn this on and then once you're ready to bleach which i'm not going to do because it's going to blast light through you'll press start and then it has this idle one done which means synapse will go from preview mode to idle mode when you're finished so it's a good thing to do okay we can exit bleaching over here all right that's all great so the next step is going to be to swap out that fc to fc cable that we're now using on the pm1 plug in your regular subject cable and by the way if you have a rotary joint you want to bleach through the rotary joint connection as well the other important thing to note is if you have a rotary joint you want to measure the power from the output of the rotary joint to the pm1 so if you were to for example use that scfc cable that you used earlier i said go from the sample port to the pm1 for people who have a rotary joint you'd want to go from the output of your rotary joint to the pm1 because rotary joints can have associated loss of signal and light power through them okay so now we're hooked up from the sample port to the regular subject so i'll turn these back on what you'll see is you know it's going to be a lot lower in terms of signal that's okay we're not pointed at anything that's bright and fluorescent and then you'll see as a result you know the q factor is very low but what are we going to do now what we're going to do is we're going to get a piece of paper scribble some highlighter on it and then we'll watch the signal change so what we want in this highlighter test which is it's a silly little benchtop test but it's helpful we want a surface that's black we want a white piece of paper and we want some yellow highlighter so scribble maybe a strip of yellow on the white piece of paper and what we're going to do is the black surface is going to be your control right because it's black it's not going to fluoresce really there's little to no reflection so you're going to take the fiber tip and maybe you know two or three centimeter okay you have fluorescent slides too that's great um but the highlighter test same deal you're going to take the fiber tip and you're going to maybe two or three centimeters hovered over the black surface so we'll turn these leds on okay and now what we're going to do is move over to the uh to the white surface and you'll see the 405 increase primarily so i'll hold shift and drag and then go back to black okay uh you get a tiny tiny bump in the 465 but what you'll see is once we go over the four uh the the yellow highlighter that the 465 jumps up dramatically so go over the yellow surface now and it goes way way way up so the relative magnitude of change here is much more on the 465 go back to black all right now go over white now black okay and now yellow perfect now back to black so the point of this test is to show you how the lock-in application is working basically over the black surface nothing too crazy is happening over the white surface only the 405 is sort of reflecting and picking up and then over the yellow both of them are going to pick up now if you have fluorescent sides which you do you can do the same thing that's actually kind of what the pm1 is doing but basically what this is showing you is okay with the same two colors shining on the same fiber i can distinguish different signals now it's just a dumb little test where okay why does it why does 405 increase over the white it works it works that way um and that's fine it is what it is it's but it's showing you that there's differences here again there was a very tiny little bump here but it's just a silly little bench top test doesn't matter in any case locking notifications looking good it's working we're happy uh with how this is functioning now one common thing i do see when people do this bench top test is if the power is too high or they get too close to the yellow what will happen is they'll end up clipping so actually let's try and do that real quick so take the fiber and get really close to the yellow yep and so you're clipping and what happens is when you clip you'll see your signal drops sometimes a zero if you're clipping all the way you get a flat line here back up a little bit you'll see once when you're not clipping that the signal returns and why is that it's because when you have a flat photo sensor line when you're saturating there's no 210 no 330 so you have no signal so you get a drop out in your demodulated signal and um it was quick but you know this will also go red if you're clipping so that's a little bit about the highlighter test now um what i want to do is just quickly press record here and take a look at that tank block structure i mentioned earlier okay two seconds totally fine it doesn't really matter what i'm going to do is click this dot dot dot over here and that's going to bring me to this history dialog also accessible through the menu history and this you can see is the recording we just did if i click previews it also has a list of previews but here's the recording that i just did um i can right click and i can say go to data folder on disk alright this is bringing us to a set location here that by the way is set in the menu preferences um but you have a d drive so you should use that as your you know data dump but basically here's the here's the structure i have this tanks folder and you have this setup right here that's the experiment name so i double click here here's my subject name and the date that it was created so this is my recording double click here and then here are my recording files now all of these constitute your recording file the most important ones are this teb and tsq file but there are very important ones here too as a matter of fact this tin file if i unzip it it's really a zip file so i can rename it so let's say you transfer uh recordings between computers or let's say you for example you know lose a copy of your experiment this tin file if i unzip it actually has copies of your experiment in them so that can be very helpful as well another cool thing about this history dialog if i right click say view data in open scope drag this over here right click the gray space size to grid press animate highlight here i'm right click maybe hide this because we don't care too much about it it's just going to replay the data kind of like the synapse flow plot again it was three seconds so nothing too crazy but you can replay the data here and for people who have videos and stuff like that you'll also use open scope uh for maybe scoring videos but we don't have a usb cam in this case so press no there um this history dialog when you go to import the data into either python or matlab which we have sdks for if i go back to the knowledge hub go to offline data analysis tools and matlab tools python tools i'm a matlab guy just because it's easier to do matrices things in my opinion well plotting's actually the easier thing that i care about but in any case you could use either of those and we have these functions to input the data and read them and for both of those functions the arguments end up being the path that you use so if i go here it's this full file path over here or you can copy the path to clipboard here and use that because if i go to notepad um i'll just paste into here you'll see that it copied the copy the file there now the most important thing is in python um when you go to import the data that these slashes need to be reversed um or double slashes it doesn't like the file path where the slashes are the um backwards slash so that's a little bit about that a little bit about open scope uh again i showed you how to do the camera earlier that's a big thing that people like to use is is a usb camera you can do up to two usb cameras uh in synapse so let's try let's go to menu edit rig right click add cam and then right click add cam now the important thing is for the second camera that you say usb id 1 so it tries to recognize it on a different usb bus all right this one is connected go to preview over here okay it's a monochromatic camera it shows up here um that's all that's wonderful uh you can change the frame rate if you want now i did notice that the free run rate was a little bit lower than 10 so you might not want to run it at like for example 20. try 10 if you get some drop frames and i'll show you in preview it'll tell you if you're dropping frames or not so here's our cam split that over to the left maybe so you know okay it's going to hover around 10. doing a pretty good job cam one all right here's our cam one and drag that over here
right click split up we got our two cameras over here that's wonderful um if it ever drops frames it'll tell you here what you'll get here if i zoom in or you know these are our cameras you'll see these are not static 10fps so the frame rate's going to vary a little bit which means that if you're using like vlc media player or windows media player it might estimate the time wrong because it'll either assume a certain fps which it's not or um you know there'll be a little bit of variability in each of the frames so whenever you need to let's say score data later on which we're not going to get into now that's something we can talk about in any case one thing i really want to show you real quick let's do a very short recording you know okay three seconds we're happy go back to that history dialogue over here right click you date an open scope if i go to view video viewer my two videos pop up here and when i press animate it'll have the time stamps of when each of the frames were grabbed more and more on that you know another at a later date the last most important thing i wanted to talk about is something called um persistence so over here you'll see i've been clicking this button but it's been hovering around this thing called persistence um now what that is is it's basically the runtime settings that you're using so if i go to preview if you recall i changed the levels to 21 and like 25 or something like that 33 and 21 okay that's great i want it to be 33 and 21 when i go back to preview or when i go to record you don't want to set that every time however if you were to make a new subject and a lot of people do you know let's call this subject one i don't have a last known runtime setting for this subject and the persistence is tracked based on the experiment name and the subject name so what it's going to do is it's going to inherit these default values to start with so if i go to preview it's 10 and 10. let's change this over quick and go to idle so when i go back to preview it's going to be 12. but let's say i go back to algernon what's it going to be well better be 33 and 21 because that's the last known setting of algernon under the experiment setup which it is so that's what the best persistence does if i pick last and go to subject one it's going to be 33 and 21 because that's the last known runtime setting okay um okay it did 10 and 12. so maybe maybe i'm a little bit wrong there let's have it as last and go to algernon okay now now it recognized it okay so maybe i just misclicked earlier but now if i say yes here it's going to use 12 and 10 because that's the last known runtime setting that i used and let's say oops that was a mistake how do i how do i fix this well there's no you know there's no indication of the settings here for the remember that revision log for the experiment but there is a known history here if i click on the history dialog and say show full history detail and i click on one of these recordings it'll it'll you know okay it doesn't have any changes here but if i go to these previews over here one of these should have okay it tells me that i changed the level here for my subject one okay but if i remember correctly okay i remember that this algernon recording had a good level that that was the correct level i wanted to use i can right click and i can say use ending state and then it's to use the settings that i had for that recording so it's going to be 33 and 21 which is what i wanted and now when i go to idle it'll hop back to best because that was the last setting that i used that's the best setting for algernon according to what i declared so that about wraps up the initial training and everything that you probably need to know before doing something like an in-vivo test that's sort of the next step and that has its own host of issues if you've seen the recordings on rz5 it's not going to be much different just make sure you measure the power make sure you're hooked up to the subject good no gaps in the cannula uh and you should be pretty good to go you know it's not like it's calculating the signal any differently a lot of this is in the manual actually the whole thing about persistence and stuff is in the synapse manual not the photometry user guide but everything we talked about is in the fiber photography user guide in reference to rz10x and the fiber photometry user gizmo
2023-06-30 14:58
