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Related Manuals for STILLA Prism6 H24000.3
Summary of Contents for STILLA Prism6 H24000.3
- Page 1 TILLA Prism6 & Crystal Reader software for the naica® system User Manual Prism6 H24000.3/H24000.6 Crystal Reader software v3.0.7.3...
- Page 2 Stilla Technologies. Stilla Technologies reserves the right to modify its products and services at any time. Information contained in this user manual is subject to change without notice. Stilla Technologies assumes no liability for errors or any damage resulting from the use of this information.
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Page 3: Table Of Contents
How to perform focus calibration? How to Pool/Unpool Chambers: VI. MAINTENANCE AND TECHNICAL SUPPORT Cleaning Decontamination Disposal To ship the instrument back to Stilla® VII. TROUBLESHOOTING For Sapphire chips For Opal chips VIII. SOFTWARE LICENSE INFORMATION Crystal Reader software license... - Page 4 Prism6 & Crystal Reader software User Manual Third-party licenses...
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Page 5: Introduction
2. Overview of the Crystal Digital PCR™ Workflow Crystal Digital PCR™ is Stilla Technologies’ next-generation technology for the absolute quantification of nucleic acids. Using cutting-edge microfluidic innovations, this technology integrates the digital PCR process in a single consumable (Fig. 1). The sample is first flowed through a network of microchannels and partitioned into a large 2D array of 15,000 to 30,000 individual droplets (Sapphire chips) and 10,000 to 20,000 droplets (Opal chips), also called a droplet crystal. -
Page 6: Intended Use Of The Naica® System
® environment. Before using the naica system, the user should be trained by a Stilla Technologies ® representative. In general, Crystal Digital PCR™ can be performed with all types of DNA sample types on the naica®... -
Page 7: Citing The Naica® System In Scientific Publications, Presentations, Seminars, Etc
Crystal Reader software • Crystal Miner software • naica® PCR MIX reagents: o naica® PCR MIX (Stilla Technologies, France) o naica® multiplex PCR MIX(Stilla Technologies, France). III. Materials and Equipment ▪ Prism6 instrument (H24000.3/H24000.6) 1 tray holder for Sapphire chips... - Page 8 Do not use the Prism6 instrument if any parts are broken, chipped, rusty, or if the power cables are damaged in any way. o Do not open the housing of the Prism6 instrument if not explicitly instructed by a Stilla Technologies representative.
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Page 9: Prism6 Labeling
For instrument shipment only follow the detailed packaging and shipment procedures provided by Stilla Technologies. Do only package and ship the instrument when instructed by a Stilla Technologies representative. Regular instrument service maintenance is recommended to ensure optimal system performance at all times. - Page 10 Prism6 & Crystal Reader software User Manual The product should be disposed of in an appropriate recovery and recycling structure. CE marking (manufacturer's declaration that the product meets the requirements of the applicable EC directives). Power on. Power off. Protective conductor terminal. •...
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Page 11: Prism6 Declaration Of Conformity
Note: Differences in USB key compatibility with the Prism6 front panel USB ports can occur. Stilla Technologies recommends to use a USB key with a maximum capacity of 8Gb.The compatibility of individual USB keys needs to be validated by the end user for functional data transfer. -
Page 12: Prism6 Installation Instructions
Prism6 instrument, is always executed by a ® Stilla Technologies’ Service Specialist. The installation includes the performance validation of Stilla Technologies Crystal Digital PCR™ specifications for all components of the naica® system, including the Prism6 instrument. At the end of the naica® system installation, Stilla Technologies... -
Page 13: Operating The Prism6 Instrument
Technical Support for any questions. The original configuration and calibration files for the Crystal Miner software are located on the Prism6 instrument by default at ”C:\Program Files\Stilla\CrystalReader\config”. Stilla Technologies does not recommend reading, modifying or deleting any of the following files: •... - Page 14 Prism6 & Crystal Reader software User Manual 2. Turn on the Monitor of the Prism6 instrument. With instrument initialization, the Microsoft Windows Login window appears. The default password is “admin” for “admin” user. Refer to Microsoft Windows User Manual regarding account features. 3.
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Page 15: Instructions For Chip Positioning
Prism6 & Crystal Reader software User Manual Press the “OPEN TRAY” button on the Crystal Reader software homepage. Alternatively, press the “Eject” button located at the front of the Prism6 instrument (Fig 1). Wait until the moveable tray is fully ejected before placing the chips for scanning. Figure 3: Fully ejected position of the movable tray. - Page 16 Up to 3 chips can be fitted into one tray holder for scanning at a time. The direction for insertion of the tray holders onto the moveable tray is indicated on the individual tray holder labels. Stilla Technologies recommends cleaning all tray holders occasionally with 70% ethanol solution, rinse with water using a lint-free wipe.
- Page 17 Prism6 & Crystal Reader software User Manual Insert the chip in the tray holder. Each type of chip has a poka-yoke corner matching the respective tray holder. Note : Sapphire tray holder - top-left corner Opal tray holder - bottom-right corner Ensure the respective chip type is pushed against the top-right corner of the slot...
- Page 18 Prism6 & Crystal Reader software User Manual Correct positioning of a chip in the tray holder. Incorrect positioning of a chip in the tray holder. The chip is lying at an angle in the tray holder and is not well attached to the top-right corner of the tray holder.
- Page 19 Prism6 & Crystal Reader software User Manual Place the tray holder on the movable tray Gently push the tray holder towards the back of the moveable tray. The tray holder is correctly positioned after the spring-loaded ball bearing (blue circle) is set in position with a distinct click.
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Page 20: Instructions For Chip Scanning
Prism6 & Crystal Reader software User Manual Correct placement of the tray holder on the moveable tray. Incorrect placement of the tray holder on the moveable tray. Retract the moveable tray for chip scanning. a) Press the “CLOSE TRAY” button on the Crystal Reader software homepage. b) Alternatively, press the “Eject”... -
Page 21: Experimental Set-Up With Crystal Reader Software
Prism6 & Crystal Reader software User Manual If different scanning parameters or experimental details are to be applied to the same set of samples for an experiment chips can be scanned up to three times within 48 hours following the first scan. - Page 22 • For an experiment using the naica® PCR MIX compatible with EvaGreen® fluorescent intercalating dye and the Opal chip select ScanningTemplate_Prism6_OpalChip_naica-PCR-MIX_Evagreen_v1.0.ncx. Note: Stilla Technologies does not recommend modifying the provided file templates. If a modification of any template file is required, please contact the Technical Support.
- Page 23 “Recent files”. To select a different scanning template, proceed to “BROWSE” and select the respective scanning template from the set of default scanning templates provided at the location: C:\Program Files\Stilla\CrystalReader\templates. The user can use the chamber details default settings or load the chamber details that are embedded in the scanning emplate. This...
- Page 24 Prism6 & Crystal Reader software User Manual feature will provide the user a faster way to set up an experiment context that will be run several times. Figure 7: Crystal Reader software pop-up window prompt the chamber details configuration that the user can load. Figure 8: The Crystal Reader software home page for the Sapphire chips.
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Page 25: Name The Experiment
Opal chips. o Enter the experiment name in the “New Experiment” field. Note: Stilla Technologies recommends establishing traceability rule for experiment naming (e.g., date prefix, chip IDs, user initials, objective of the experiment; 20210507_04527983- 04568924-04698435_ABC_valid_6plex). -
Page 26: Edit Experiment Details
Prism6 & Crystal Reader software User Manual o The “Comments” field can be used to add Edit experiment details: any information pertaining to the experimental record. Figure 11: Enter fluorophore and target names in the “Experiment Details” interface. o Go to the “Experiment Details” button in the left panel, then enter for each detection channel (“Blue”, “Teal”, Green”, “Yellow”... - Page 27 Figure 12: Select the relevant “Embedded Files” for the experiment. Note: The Image Analysis Configuration File (“.yaml”) is mandatory in the experiment. When selecting a scanning template provided by Stilla®, an Image Analysis Configuration File is already set for the experiment.
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Page 28: Check The Scanning Parameters
Configuration File that is optimal for the majority of experiments prepared by the user. The specific files for different applications are available on the Monitor at this location by default: “C:\Program Files\Stilla\CrystalMiner\config” o In the “Plots Configuration”, the user can load the Crystal Miner plots configuration here to have it ready to use in the “.ncx”... -
Page 29: Step (2 And 3) - Select The Chambers To Scan & Define Chamber Context
Prism6 & Crystal Reader software User Manual o To find the optimal LED exposure times for new experimental conditions, the user may create a control experiment in which only one chamber is activated, and a few scans are run until an optimal set of exposure times is found. o When at least one chamber of the experiment has been scanned in the experiment, the LED exposure time should not be further edited to ensure that all the chambers of the experiment share the same scanning parameters. - Page 30 Prism6 & Crystal Reader software User Manual To navigate from one chip holder to another, click on the left or right arrows around the chip holder counter at the bottom (Fig 13). Figure 15: Chip holder counter. o Click on the “validation icon” (located below the chip holder layout) to validate the selected chambers.
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Page 31: Step (4) - Launch The Scan
Prism6 & Crystal Reader software User Manual For the dilution factor, in case no value is specifically added, the final concentration in copies/µL will correspond to the number of DNA copies for each µL in the whole 25 µL of reaction mix for Sapphire chips and 7 µL of reaction mix for Opal chips. -
Page 32: Check Chamber Image Quality
Prism6 & Crystal Reader software User Manual Check chamber image quality The scan can be canceled at any time, but you might lose some scanned data. Editing the experiment context is deactivated during the scan process. o If several tray holders have been selected for the scan, the scanning process is split in several steps: •... - Page 33 “<ExperimentName>.ncx”. Default output directory is: “%USERPROFILE%\Documents\Stilla\CrystalReader” Note: Quality flags only apply to the Blue LED channel. Stilla technologies recommends to visually inspect all the other the LED channels. Stilla Technologies recommends to first continue to check the scanning performance by looking at the image quality.
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Page 34: Step (5) - Check Image Quality
Prism6 & Crystal Reader software User Manual 4. Step (5) - Check image quality o Click on the quality flag of a chamber to explore the respective chamber image in detail. Figure 21: Overview of a Sapphire chip chamber image in the “Blue Channel” detection channel in the Crystal Reader software. - Page 35 Prism6 & Crystal Reader software User Manual Figure 22: Zoom-in into a chamber image in the Blue detection channel (all negative droplets should be visible in the Blue channel image) in the Crystal Reader software. o The Grayscale Histogram tool (bottom right) might help you to appreciate the distribution of pixel intensities expressed in RFU (Relative Fluorescence Unit), where 0 RFU indicates –...
- Page 36 Prism6 & Crystal Reader software User Manual By dragging & dropping in the histogram with the left mouse button, you can set the minimum and maximum intensity cursors and draw an interval. The pixels with RFU values included in this interval will be highlighted in orange color in the chamber image. In the following example, we select the interval 24576-37632 RFU, which reveals the positive droplet population: This tool helps to detect time exposure issues and provides an indication of separability...
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Page 37: Advanced Functionalities
Prism6 & Crystal Reader software User Manual corrected by checking that the chip holder is clean and the chamber is well placed). ▪ “Number of analyzable droplets”: the higher the number the better the confidence in predicted concentration results. Note: Saturated droplets and droplets covered by artifacts are not analyzable. -
Page 38: How To Rescan All The Chambers Of The Experiment
Prism6 & Crystal Reader software User Manual How to rescan all the chambers of the experiment? How to scan additional chambers? How to rescan only a subset of chambers? Settings: non-logged user Irrespective of the option chosen, if there is at least one already scanned chamber when the “SCAN” button is clicked, this window will be displayed: Figure 25: Default rescan window (chambers to be rescanned are highlighted in blue color) in the Crystal Reader software. -
Page 39: Settings: Logged User With "Basic" Profile
Focus Value (mm): z-distance to the imaging plane used for image acquisition (set by the user). Prism6 Serial Number (SN): unique serial number of the Prism6 (set by Stilla Technologies). • “Focus Calibration” button: advanced functionality to automatically adjust the... -
Page 40: Settings: Logged User With "Manager" Profile
Prism6 & Crystal Reader software User Manual Unless modified after Settings: logged user with “Manager” profile default software installation, default “Basic” account is created with the login “guest” and the password “guest”. Figure 27: Settings page for a logged user in the Crystal Reader software. A logged user has the same rights as a non-logged one, except that his/her user preferences for the input/output storage directories will be saved even after quitting Crystal Reader software. -
Page 41: How To Perform Focus Calibration
Prism6 & Crystal Reader software User Manual Figure 28: Settings page for the logged manager in the Crystal Reader software. A user with the “Manager” profile has the same rights as a “Basic” user and has the following additional rights: •... - Page 42 Prism6 & Crystal Reader software User Manual o Assuming that the user is already logged with the “Manager” account and that a chip with a chamber of interest is already inserted in the Prism6 instrument, access the SETTINGS menu, click on the “Focus calibration” button, then select the chip model of interest (Sapphire chip or Opal chip).
- Page 43 Prism6 & Crystal Reader software User Manual Figure 30: Example of selection of nine chambers to calibrate the focus for the Opal chip in the Crystal Reader software. o Click on the “SCAN” button on the bottom to launch the focus calibration process. A progress bar is then displayed with the estimated remaining time.
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Page 44: How To Pool/Unpool Chambers
Prism6 & Crystal Reader software User Manual Figure 31: Example of the result of focus calibration for the Opal chip in the Crystal Reader software. 4. How to Pool/Unpool Chambers: Figure 32: Pooling feature of the Crystal Reader software. - Page 45 Prism6 & Crystal Reader software User Manual Figure 33: Detailed view of a chamber in the Crystal Reader software. An additional feature where users can pool multiple selected chambers containing the same sample called the “POOLING CHAMBERS” is available in the Crystal Reader software. Pooling a set of chambers in which the same sample has been loaded allows to gain both detection sensitivity and quantification precision.
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Page 46: Maintenance And Technical Support
Cleaning Maintenance operations of the naica® system should be executed by a Stilla Technologies Technical Specialist during a visit on-site or by a return shipment of the device to Stilla Technologies premises. Stilla Technologies cannot be held responsible for any intervention or modification done by the user on devices of the naica®... -
Page 47: Decontamination
The Prism6 instrument should be packed and shipped back to Stilla® only after a Stilla Technologies Service Specialist has deemed it necessary. If shipping the Prism6 is required, use all the original packaging and cables provided upon reception of the naica®... -
Page 48: Troubleshooting
Please use the scanning templates provided by Error: current Image Analysis Stilla Technologies accessible at Configuration File (.yaml) is not designed to be used on this scanner type. Please https://www.stillatechnologies.com/technical- resources/naica-system-prism6/. Please ensure ensure the consistency between the the consistency between the “.yaml” file and the “.yaml”... - Page 49 Prism6 & Crystal Reader software User Manual Error: selected Spillover Compensation Matrix file (“.ncm”) uses a Please use the scanning templates provided by different number of channels than the " Stilla Technologies accessible "current experiment. Please check the https://www.stillatechnologies.com/technical- consistency of these elements. resources/naica-system-prism6/.
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Page 50: For Sapphire Chips
Prism6 & Crystal Reader software User Manual For Sapphire chips Observations Possible cause Recommendations Check that the crucial partitioning step is included in the PCR program used (1 step). The partitioning step did not occur If the problem persists, please extract the live and system logs (refer to the section “How to use the Geode Software User Interface”... - Page 51 Prism6 & Crystal Reader software User Manual Presence of an out of focus sub- Autofocus failed during scanning the sub- image. Rescan the concerned chamber. image There are two or more droplets (crosses) Manually inspect the droplets, in case of red crosses, the software automatically instead of one (oversegmentation) or one Oversegmentation or rejests the droplets, no action is required.
- Page 52 It is also been heated up for too long possible to use the Template PCR program "FAST-Template Stilla PCR 45 cycles.js ". Aggregates can also occur depending on Rescan the chip immediately after the first testing conditions...
- Page 53 Prism6 & Crystal Reader software User Manual Shiny dust particles on the external film of the chip. Clean the foil with lint-free wipe and re-scan Presence of dust particles on the chip foil the concerned chamber. Large air bubbles in the chamber Make sure to pipet 25 µL of the reaction mix.
- Page 54 Prism6 & Crystal Reader software User Manual The whole chamber is out of focus Verify that the chip and/or chip holder is positioned flat. The chip and/or the holder is not well A foreign particle might be present between the positioned chip and the holder, forcing the chip to be tilted.
- Page 55 Prism6 & Crystal Reader software User Manual The chamber is not optimally filled The chamber is still analyzable as the The sample volume loaded in the chamber partitioning step was successful. Depending on was low. the assay, it is the user discretion if the number of analyzable droplets is sufficient.
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Page 56: For Opal Chips
Prism6 & Crystal Reader software User Manual For Opal chips Observation Possible cause Recommendation A low average number of droplets partitioned During the loading of the chips, multiple droplets could have been generated in the Make sure that the electrostatic pen is working. inlet port. - Page 57 Prism6 & Crystal Reader software User Manual Refer to the IFU for correct placement of the Opal The Opal chips were not placed following the chip in the Geode before starting a new run. recommendations provided in the IFU. If the Opal chip PCR caps are not properly placed Empty chambers/non-injected chambers.
- Page 58 Prism6 & Crystal Reader software User Manual Air bubbles in the chambers. If the Opal chip PCR caps are not properly clipped on the Opal chips, a lower volume of mix The Opal chip PCR caps are not (or any volume of mix) will enter the chamber. properly set on the chip.
- Page 59 Prism6 & Crystal Reader software User Manual Visible traces on the chamber Repeat the procedure of cleaning the Opal chip The traces could be due to the foil with a lint-free tissue sprayed with the partial drying of the antistatic antistatic spray.
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Page 60: Software License Information
Prism6 & Crystal Reader software User Manual VIII. Software license Information 1. Crystal Reader software license ©2015-2021 Stilla Technologies. All rights reserved. For Research Use Only. Not for use in diagnostic procedures unless specified otherwise by domestic registration. 2. How to view the software version? o From the HOME page of the Crystal Reader software, click on the “ABOUT”... - Page 61 To view the license information, please visit the third-party websites or check the Crystal Reader software and Crystal Miner software installation directory (by default in “C:\Program Files\Stilla\CrystalMiner\licenses”). Note: The license information of all the third-party software components is also accessible in...
- Page 62 Villejuif Biopark 1, Mail du Professeur Georges Mathé 94800 Villejuif, FRANCE Phone: (+33) 09 82 29 50 50 North American Office Stilla Technologies Inc. 66 Cherry Hill Drive, Suite 110 Beverly MA 01915, USA Tel: 1-833-888-0150 For sales related queries...
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