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3Brain BioCAM X, User Manual

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3Brain BioCAM X User Manual Download Page 33

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Quick analysis and save of results

As a first step, we perform a spike detection on the loaded data. Choose Analysis > Peak Detection 

from the Main Menu or alternatively press Ctrl+P. On the new opening window, simply leave the default 
parameters and click OK and then wait for the analysis to be accomplished.

Once finished, the BXR-field in the Info panel turns yellow to indicate that there are unsaved data. To 

save data do one of the following:

• 

Click on the icon right to the BXR field in the Info panel;

•  Click File > Save

•  Press Ctrl+S

Once you have saved the data, the Experiment tab name indicates the BXR-file name and the BXR field 

in the Info panel updates too.

Summary of Contents for BioCAM X

Page 1: ...1 Welcome to ...

Page 2: ...2 Last updated 25 09 2019 User Guide Essentials ...

Page 3: ... BioCAM X 21 Desktop host PC 21 Laptop host PC 22 Plug the BioChip 23 Set up a non pre configured host PC 23 Verify proper functioning 24 Quick guide to your first use 25 Basic concepts 25 Visualization of data 26 MEA Viewer control 27 Data formats 28 Online mode Record mode 28 Important notes 28 Open recorder 29 Visualize live data 30 BioChip Calibration 31 Record live data 32 Offline mode Playba...

Page 4: ...of relevant channels 37 Visualize Instantaneous MFR 38 Visualize Raster 39 Troubleshooting 40 Electrodes with no signal saturation 42 BioChip not properly initialized 44 Not working columns 45 BioChip with dirty surface ...

Page 5: ...Introduction 1 ...

Page 6: ...trates Each microelectrode can be made by different materials e g Pt IrOx TiN and it is individually wired on chip and connected to an external amplifier and data acquisition DAQ instrument Due to the need of this MEA technology of individually routing on chip each electrode space constraints and wiring encumbrance impede the realization of dense and large electrode arrays Thus for conventional ME...

Page 7: ...ngs from a large signal bandwidth that includes field potentials and spikes Instead of implementing an AC coupling solution that would require large areas for the integration of adequate capacitors the BioChips in pixel circuit integrates an au to zeroing circuit that is regularly calibrated to the electrode DC voltage and that subtracts this cali brated DC voltage from the electrode signal before...

Page 8: ...At a glance 2 ...

Page 9: ...to investigate electroactive prepara tions The 3Brain s BioCAM X platforms was tested so far for in vitro electrophysiological experiments on neuronal cell cultures brain slices retina preparations and cardiac cultures Electrophysiological signals ranging from slow field potentials to fast single cell spiking activity can be recorded simultaneously Examples of recordings provided by different labo...

Page 10: ...le connection PCB the printed circuit board substrate of the BioChip Different colors are available and according to the layout of the CMOS MEA Glass ring borosilicate glass ring defining the reservoir External diameter 28mm 1 7 64 in internal diameter 25mm 0 63 64 in height 5mm 0 13 64 in Reservoir chamber for the bath solution used for the biological preparation The volume of solution that can b...

Page 11: ...hip cartridges and to acquire and pre process large volume of electrophysiological data before sending it to the host PC Magnetic plate Lock button Peltier Element BioChip bay Lock button two position button for locking end position or unlocking mid position the BioChips BioChip bay bay for inserting the BioChip and connecting it to the BioCAM X Magnetic plate ferromagnetic stainless steel to atta...

Page 12: ...ely behind the BioChip slot a protective movable Bay Bar rier blocks accidental overflows of liquids that might get in touch and damage the internal electronics Behind the Bay Barrier the BioChip connector allows to connect the BioChip s contact pads to the internal circuitry Electrical contacts are established only once the locking system is activated Reference connector connector for the pseudo ...

Page 13: ... a Camera Link acquisition board The typical configuration is as follow tower desktop not shown BioCAM X with BioChip Desktop host PC with BrainWave X Laptop PC When connected to a laptop PC you need an adapter to connect the BioCAM X to the host PC Such adapter is a Thunderbolt Camera Link adapter box that encloses the Camera Link acquisition board The typical configuration for a laptop hosting P...

Page 14: ...ls and for some controls can be missing Panels dockable panels that are automatically updated according to the currently selected experi ment loaded into the Workspace Panels allow you to modify the experiment s options and parame ters and can be shown or hidden by choosing the Window menu on the Main Menu Left Status Bar notifies you about ongoing operations Workspace arena for visualizing throug...

Page 15: ...Precautions 3 ...

Page 16: ...96 and let it dry Execute the same procedure for all the BioChip parts but for the BioChip reservoir and in particular for the BioChip con nector pads 3 In case after the cleaning with ethanol there are still doubts that some liquid could have been penetrated into the BioCAM X do not switch on the system for at least one day allowing the liquid to be completed dried and preserving internal circuit...

Page 17: ...n These methods might deteriorate the CMOS devices resulting in malfunctioning or in reduced lifetime For the BioChip sterilization please refer to the Sterilization procedure for BioChips Maintain the pH of the electrophysiological solutions used for neuronal cultures or brain tissues pos sibly at physiological conditions 7 7 5 Important changes in the pH of the solution might damage the electrod...

Page 18: ... chip so it is suggested only if after a normal cleaning procedure the chips still present dirtiness and in any case it has to be performed very mildly and carefully Finishing and storage Biochips can be dried by using a gentle flux of Nitrogen air do not directly expose the recording area to the flux to avoid potential electrode damages Alternatively let the BioChips dry on a bench by covering th...

Page 19: ... ring itself by using a tissue soaked with ethanol 96 and put inside sterile plastic petri dishes 2 Fill the reservoir completely with ethanol 70 Also dip with the same solution the border of the glass ring the tiny upward oriented side of the ring Hence wait for 20 minutes 3 Suck the ethanol with a pipette or with a vacuum pump always using sterile tips 4 Fill 3 4 of the reservoir of the BioChips...

Page 20: ...Get started 4 ...

Page 21: ...e power port located in the back of BioCAM X and then connect the power supply into an electrical outlet Switch ON the BioCAM X by pressing the power button on the back The BioCAM s LED1 should turn ON 2 Plug the power supply cable into the power port located in the back of the Thunderbolt Camera Link adapter box 3 Connect one end of the Camera Link cable into the Thunderbolt Camera Link adapter a...

Page 22: ...AM X end is approx imately 7mm 1 4 in If the BioChip does not enter till the ending position try to push the BioCAM X s lock button till its mid position to release the locking system and then try re inserting the BioChip 2 Push the Lock button in the BioCAM X to its end position to lock the BioChip to the BioCAM X con nector On BrainWave X software the BioChip LED icon in the Device Status Bar sh...

Page 23: ... the software automatically restarts Verify that in the BrainWave X s Right Status Bar there are no error message If you see a message like No detected acquisition board it means that either the acqui sition board is not installed properly in the PC or its driver are not installed In the latest case repeat step 1 4 Follow the instruction in Install the BioCAM X to verify that all the components ar...

Page 24: ...24 Quick guide to your first use 5 ...

Page 25: ...ration or whether you are playing back data previously recorded These two different scenario are referred as online mode and offline mode respectively The term Experiment can be used both for an online and an offline experiment When a new Experi ment is started online or open offline its data is loaded and displayed in the BrainWave X s Workspace area More Experiments can be loaded during a single...

Page 26: ...vity by converting the channels voltage values in your MEA to pixel colors This is done according to the below color scale and settings At a specific time location in your recorded Ex periment the MEA Viewer gives an image representation of the activity When instead you visualize live data acquired from the BioChip or when you playback recorded Experiments the MEA Viewer refreshes continuously thu...

Page 27: ...EA channels or a temporal subset of those data In what follows you will learn to record plain raw data file BXR stands for Brainwave eXperiment Result data file and contains discrete data obtained by analyzing and processing the raw data BXR files can for instance contain the timestamps of the detected spikes In the following section you will learn to create a BXR file starting from a BRW file Con...

Page 28: ...nhance speed A RAID0 configuration should not be confused with the mirroring RAID1 configuration that allows to copy your data on two physical hard disks thus protecting your data from loss due to hard disk failure RAID0 configuration does not help protecting your data a failure of any of the two underlying hard disks will cause a data loss Hence you should always backup your important data For de...

Page 29: ...wer starts refreshing and displaying data 2 Click on the MEA Viewer to select individual channels or Shift click to select more channels For each selected channel a new chart is plotted on the right showing the voltage data being read out from that channel 3 Use the Chart panel to adjust channels charts Two controls are available on the Chart panel for both the time X and amplitude Y axis scale va...

Page 30: ...anel To perform an automatic calibra tion you first need to start an acquisition by clicking on the Play button and then to click on the BioChip Calibration button The procedure will take from few tens of seconds up to roughly a minute depending on the BioChip conditions If automatic calibration is not satisfactory you can perform a manual calibration To access this feature you need the Chip Calib...

Page 31: ... a disk pool configured with RAID 0 striping If your order included a pre configured host PC the disk partition where you should record your file is typically labeled with LiveRec or RAID0 Once you chose the path by default Brain Wave X selects for you the file name but you can modify this by typing in the Name field 5 Choose the length of the experiment you want to record by bearing in mind that ...

Page 32: ...iment opens as a tabbed document The tab name is the name of the BXR file as sociated to the BRW file Since you have open a BRW file and no BXR file has still been created the tab name will be in the form Untitled X being X a progressive application session wide number Hence if this is the first file you open in this session it will be named Untitled 1 The offline Experiment tab and the panels are...

Page 33: ...ult parameters and click OK and then wait for the analysis to be accomplished Once finished the BXR field in the Info panel turns yellow to indicate that there are unsaved data To save data do one of the following Click on the icon right to the BXR field in the Info panel Click File Save Press Ctrl S Once you have saved the data the Experiment tab name indicates the BXR file name and the BXR field...

Page 34: ... the level of activity Chart bars indicating detected spikes Play button Speed control Timeline cursor a red overlaying rect angle with central left and right markers 2 Click Timeline bar in corrispondence of the red line near 0 5s 1 Click MEA Viewer on channel 24 9 to open its chart The timeline cursor centers at that position MEA Viewer and chart refresh accordingly Try to move to other spatial ...

Page 35: ...35 Charts Time bin Timeline cursor width Charts width MEA Viewer Bin setting bin to integrate for colors Charts overlay rectangle width Understanding main controls affecting graphs ...

Page 36: ...ntains a colored map representing the activity on the entire MEA as global MFR For each channel the global MFR value is converted into a color according to the below color scale 3 Set the Range definition left and right values to 0 200 and 4 000 spk s respectively In this way we consider only those channels whose global MFR ranges between such values The number of in range channels should be 1135 ...

Page 37: ...on successive small temporal bins To plot the Time MFR 1 Right click on Channel Selection panel then choose Select Channels Group NewGroup to select all the channels belonging to the newly created channels group An instantaneous MFR chart is plotted by summing up together all the selected channels and binning according to the Bin size setting in the Chart panel To zoom the MFR chart 2 Click on the...

Page 38: ...ter to 2pt in order to have a more defined raster 3 Zoom on time axis by using the Timeline bar control and moving the aside handlers A time raster chart is plotted Visualize Raster The time raster is another common tool used to observe activity on your data ...

Page 39: ...39 Troubleshooting 6 ...

Page 40: ... top left top right and bottom left traces or no signals right image bot tom right trace Causes Saturation arises i when the input signal amplitude exceeds the operational range of the amplifiers integrated inside the BioChip s CMOS or ii when the amplifiers working range is not properly set In the first case this could be due to invalid signal input for instance in the second case a wrong calibra...

Page 41: ...blem is not solved check following scenarios and remedies S3 Pseudo reference electrode is dirty or it has not been cleaned for a relatively long period Proteins and impurities can attach with time to the reference electrode and degrade the reference performances causing few or many channels to exhibit persistent saturation Check section BioCAM X handling and use how to clean the pseudo reference ...

Page 42: ...ion in BrainWave e g by clicking Play or Record buttons If the con nection to the BioChip is not in place or it is compromised the initialization of the chip will fail Possible scenarios and remedies Scenario Remedy S6 BioCAM locking system see section Plug the BioChip was in the unlocked state when acquisition was initiated Stop the acquisition make sure that the Bio Chip is properly inserted til...

Page 43: ...ps exhibit the same problem go to next scenario S8 BioCAM X bridge module which is responsi ble to connect the BioChip to the BioCAM is dirty or damaged Take one BioCAM Contact Cleaner and follow these instructions to try to clean the BioCAM X bridge module 1 Soak the cleaner on the marked area with pure ethanol 96 2 Unlock the BioCAM locking system 3 Insert the cleaner making sure it is inserted ...

Page 44: ... a non working conditions then the BioChip is in herently damaged at that location In most cases it is still possible to record from the remaining working electrodes Causes One or more of the lines that go from the BioChip to the BioCAM X exhibit a faulty connection This issue typically occurs between the BioChip contact pad s and the BioCAM X bridge module integrated inside the mechanical locking...

Page 45: ...eaks have a shape quite different from that of a real spike but some might still look similar Causes BioChip CMOS surface is dirty which makes some electrodes unstable Possible scenarios and remedies Scenario Remedy S9 BioChip electrodes are dirty of debris and or more likely of dust particles While the chip is connected and is filled with saline solution start acquiring and visualizing incoming d...

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