RapidPick - Hudson Robotics
Contents
1. 12007 15 48 32 24Jul2007 15 48 53 source Plate Well ID Target Plate Row Rearray 24Jul07 143952 EN 1 1 E 261107 123149 Lo 0000000001 2000000000 0000000001 0000000001 0000000001 0000000001 0000000001 0000000001 0000000001 0000000001 0000000001 0000000001 0000000001 0000000001 0000000001 0000000001 0000000001 0000000001 0000000001 0000000001 0000000001 0000000001 10010 00 00 00 0 00 00 00 00 00 de le fe le le PPP Pee Sw co A a t m Ko b 1 0000000003 000000000 3 000000000 3 200000000053 000000000 00000000053 2000000000 0000000003 000000000 3 0000000003 20000000003 000000000 00000000053 000000000 0000000003 000000000 3 0000000003 20000000003 000000000 3 00000000053 n m A m m Mm oo m eu rxrucxmrumcmU LTFu Uu xc 1 pu oom 4 ul2007 2412007 24112007 4 ul2007 eq ul2 7 4 ul2007 24112007 4 ul2007 24112007 4 ul2007 24112007 24142007 4 ul2007 24142007 24 12007 24112007 4 ul2007 24112007 24112007 4 ul2007 24142007 15 48 54 15 48 36 15 48 37 15 48 38 15 40 59 15 48 40 15 48 41 15 48 42 15 40 44 15 48 45 15 40 46 15 40 47 15 40 48 15 40 43 15 48 51 15 48 52 15 48 53 15 40 54 15 40 55 15 48 56 15 40 57 Exit The Source Plate ID and wells are shown with their Target Plate s ID and wells Se2. a comprehensive set of log files with a built in viewer to provide easy user review of colony picking source vs target plate logs and re arraying logs It offers a convenient masking utility that permits the user to employ colony plates of varying well patterns This user manual describes the operation of the RapidPick as a complete system For information regarding the usage and features of the individual components please refer to the user manuals provided for each of those instruments Section 1 VVorkcell Operation 1 1 Startup All instruments must be powered and connected to the computer prior to starting the software packages The desktop contains two main icons SoftLinx V Hudson s Protocol Editing Software used to run the PlateCrane and RapidPick Lite protocols Picker CP7200 s operating software The CP7200 picker software should be started prior to running SoftLinx The picker must also be on before this software is activated The picker software is covered in the CP7200 manual Clicking on the x will start SoftLinx V Look ix E SoftLine V Protocols x 122 E r 1 m Pick to Deep Lid Target 1 B Pick to Desp No Lid Target y New Protocol Open Protocol Documents 15 Pick to Shallow No Lid Target 1 Rearray to Deep_Lids to edit a protocol 2 8 Rearray to Shalow_lids Desktop y Pl j t My Documents all Manage Instruments My Computer
3. camera is connected Check the focus on a colony plate by opening the Interactive Picker Imaging program Check the CP7200 manual for details Check all pins for bends and ensure that they are installed properly Go through the CP7200 calibration procedure Use the white mounting block whose height is closest to agar levels of source plates while in the source nest NOTE Failure to use a similar height block will cause all pins to be off by a very small distance Do atest pick after a successful calibration procedure If colonies are still off contact Hudson Robotics for advice 16 The picker seems to be picking colonies accurately but colonies are having issues grovving Ensure that all target plates are sterile Do manual picks with similar colonies and target plates to ensure proper growth Use the picker pins to do so Ensure the water source is sterile Flush a full bottle of clean water through the picker wash station Ensure that Ya of a picker pin is going into the heater station during sterilization If not raise the heater station until this is fulfilled by removing the back of the picker with a 3mm allen key and loosening the station to allow the heater to be raised Use the recommended wash settings of 800 and dither of 8 Ensure the pins are not bringing any water from the wash station to the source plate If so remove the back of the picker and twist the white knob of the water station such
4. ForPlate MovePlate from Stack4 Stack5 to RapidPick Target_Deep Well RapidPick S PickColonies P Rearray PlateCrane 1 MovePlate ZOJ 1 MovePlate MovePlate from Stackz to RapidPick Source_Shallow Lidded MoveCrane Moveabsolute RemoveLid ReplaceLid ET 028 1 OpenGripper RemoveLid from RapidPick Source Shallovi to Source LidNest 1 CloseGripper Beginincubate Endincubate Readinput WriteOutput 2 Main Picking Loop Y O Of Replace the Target Plate if necessary OL Replace the Source Plate if necessary Only replace if a Target Plate is present O 10 22 2010 1 18 37 PM PlateCrane Getting plate from Stack4 8 10 22 2010 1 18 36 PM Activity InstrumentActivity State Executing ID 62 10 22 2010 1 18 36 PM Activity RegionActivity State Executing ID 53 a 10 22 2010 1 18 36 PM Activity Variablelnitialization State Closed ID 2 10 22 2010 1 18 36 PM Activity VariableTnitialization State 1D 2 sel Start e SoftLinx Y 2 ar x e 1 18PM Each rectangular box in the protocol display represents a distinct action or step that 1s performed by an instrument in the system They are executed from top to bottom with the currently executing step highlighted in GREEN This enables the user to keep track of the protocol s progression Additional instrument status messages can also be seen in the Messages box located at the bo
5. RapidPick Colony Picking and Rearraying User Manual ee A Lu o 8 v z es if ya k z Hudson 10 Stern Avenue Springfield NJ 07081 Tel 973 376 7400 Fax 973 376 8265 Mrod C MOs e 000000 3 Section L Workce Operaio ienen T dadas 4 A ssn 4 1 ar n onun ENE baa aa l RoLa 6 123 rolocol Exodullonuu Aled aa a a 7 A Los m a s A a nalar 8 Section 2 Developing and Editing Protocols 11 N A D o 11 2 2 TOLOCOL Emp yaa aii 12 2 3 Rapid Pick SoftLinx 13 27 Ficking ome A a 15 70 Commons bun 16 Introduction Hudson s RapidPick workcell is a customizable automated colony picking and rearraying solution fit for any users needs The RapidPick workcell comes with multiple options to fully automate and optimize the colony picking process The RapidPick contains the following components CP7200 Colony Picker e PlateCrane EX Robot Arm PlateCrane Magazine Base with 5 Stacks Additional components for the RapidPick include Second PlateCrane Magazine Base with 3 5 Stacks Microl10x media dispenser with 4 way valve RSH 4000 microplate sealer UV light sanitation system Liconic Incubator Other components may be added at the user s request beyond those listed The RapidPick includes Hudson s SoftLinx V Protocol Editor for instrument integration and
6. access the system modify protocols or repeat the run 12 2 3 RapidPick SoftLinx Steps 4 RapidPick El Dick Colonies dE Rearray amp Scan Plate abi Segmented Pick af Clean Needles dE Prompt Manual Reset The RapidPick interface has multiple steps that can be used in a SoftLinx protocol Each one 1s shown in detail below Pick Colonies The basic colony pick as done by the CP7200 The following window will appear when the step is placed or double clicked This allows for customization of parameters to optimize the pick Pick Configuration Input Scheme Output Scheme Picking Order Largest to Smallest Smallest to Largest Fastest Pick Area Options Use Picking Segment Edit Segments Browse Limit number of Colonies to Pick Pad Wells Not Picked up to Limit Imaging Parameters Use Custom Image Parameters Pros Parameters which are customizable are as follows Picking Order Colonies are picked either by size or as fast as possible Picking Segment Allow the use of an additional filter in which to focus the colony pick Picking Segments are discussed in the next section 13 Limit number of colonies to pick Maximum number of colonies to pick within this scan Pad Wells Reserve the maximum number of wells that colonies are picked into regardless of whether or not those wells were inoculated For example if the picker is told to pick 12 colonies but detect
7. anners and DefaultEnb96 as a template for rearray functions which do use barcode scanners The output scheme shows the same options as the picker and pick colonies segmented picking steps Segmented Pick Runs multiple picks in sequence employing a different segment every time Up to 12 segments can be scanned on a single plate in succession Creating segments are discussed in the next section Input and output parameters with the exception of multiple segments are the same as in colony picking Scan Plate Allow for the colony picker to prescan the plate and save the number of colonies scanned This information can then be used within protocols for additional plate processing such as throwing out plates which have fewer than X colonies or only processing plates which have Y or more colonies Clean Needles Force the picker to clean and sanitize all 20 pins Prompt Manual Reset Stop the protocol and allow the user to place in a new petri dish into the source nest Petri dishes must be manually moved into position 14 2 4 Picking Segments The Pick Colonies and Segmented Picking commands allow users to focus the picking commands onto specific areas of a plate Segmented picking allows users to pick out of up to 12 segments in sequence on a single plate Access to creating segments can be found when editing Pick Colonies or Segmented Picking steps or when the user accesses the setup screen of the RapidPick interface
8. ction 2 Developing and Editing Protocols 2 1 Protocol Editor SoftLinx V Protocol Editor allows the user to create and modify the protocols to be run by the system The menu is accessed in SoftLinx V s main screen lt a ie a Please select Jp Manage Instruments to set up the instruments in your workcell The user can either create a new protocol or open and edit one of the RapidPick s template protocols Each available instrument and activities are displayed in the toolbar on the left of the screen Managing variables comments and other functions are available in the toolbar on the top of the screen Refer to the SoftLinx V help file for details about protocol modification Q OD Pick to Deep No Lid Target x O Delay Protocol Pick to Deep No L GE Run VBA Script Run Program Expand All Collapse All sa Parallel Processes Region OA Conditional Statement 4 Loop Process 45 RapidPick Crane Plates w Picker 4 1 8 ONLINE EJ SoftLinx v 11 2 2 Protocol Template Each SoftLinx RapidPick Protocol is built using the same template and has 3 sections Initial Loading of Plates Main Process Final Cleanup The Initial Loading of Plates section may consist of the following Preparation of the target plate Target plates are filled by the Micro10x or prefilled prior to protocol execution Lids are removed if they exist on the target plate Targe
9. in SoftLinx Define Pick Segments New Segment Load Segment Save Segment Scan Plate Click Scan Plate to get the plate image Use the left mouse button to create segments Use the right mouse button to delete segments Save segments to use in SoftLinx Protocols for greater control in picking Segments are Last Loaded Segment File The user can start with a fresh plate image and create a new segment then save it using the Save button The directions on creating the segment are found within this window Segments are additional filters to image parameter masks which are created within the CP7200 software It is suggested that one segment box 15 created and saved to a PA file then call up that file within a segmented pick step to perform picking in order 15 2 5 Common ssues The Picker softvvare does not connect to the instrument or shovv an Online status Ensure the picker is on before the software 1s activated Ensure the picker communication cable is connected to COM 1 of the computer It cannot be connected to any other COM port Ensure that wish84 exe is NOT running prior to starting the picker software and ensure that no other picker software windows are running This can be verified within Windows Task Manager Ensure window firewall is not blocking wish84 exe The picker is barely missing colonies by a few mm Ensure the camera cap is completely off and the
10. lected from the list of wells View Colony Plate List of Target Plates List of Colony Trays Dw Colony10 Colony Test d3 Select from Du Colony12 Colony _Testoso Either Target Dw Colony14 Colony 5051 1 Enn Colony15 Colony Test zz Plates or Colony DW Colony 15 Colony Test053 Trays to View Colony 17 Colony _Test054 Picked Colony TESTAPRUN Colony 5055 Locations Colony_Test056 Colony_Test057 MULL 0000000005 Click on any row to view that Picked Colony Well Target Plate Coord Y Eoord Gl Dw Colory16 538 10 199 30 5140017 H12 Dw Colornyl6 1024 30 250 10 26112007 11 Dw 1 1166390 32140 25102007 H10 L A Color E 17 510017 Dw Colorw16 56 25Jul2007 HOS Dw Color E E 1503 26112007 HO Dw Enlunu1E 1515 60 26 112007 Dw Colorny16 1815 90 26 112007 Lu 1 1693 40 25Jul2007 H 4 Du Colony16 1404 10 25142007 HOS Du Colony16 369 00 26 142007 HO Dw Color 6 l 388 90 5140017 pind Para T 1 1 4000 Pr AC 1 Janay Selected Colony Picked Colonies asa The user can select from the lists of Target Plates or Colony Trays in the upper right area of the form to display that item s data in the grid at the lower right B View Rearray Logs Similar tabular data is available from rearraying operations that have been run Rearray Log Rearray_24Jul07_143952 log Select a log File to Date Tn 9 24
11. s only 8 8 wells are inoculated and 4 wells are reserved This is useful when inoculating multiple plates into one target well where order of rows may be vital Custom Image Parameters Custom Imaging Parameters developed from and used by the picker software can be implemented here These imaging parameters overwrite the default parameters within the picker and are implemented in the protocol Note that the default parameters originally within the picker software are overwritten It is recommended that users save ALL parameters made for their bacteria Output Scheme Specify how colonies are placed in the output plate Both Pick commands and rearray commands allow customization on how the output colonies are arranged For sample custom output files access C Picker PlaceTestFiles Note that custom files may list less than the maximum number of wells but may NOT list any wells that do not exist on that plate In addition place test files can name the same well multiple times for multiple inoculations of the same well The output scheme options mirror those found in the picker software and are used in the rearray and segmented pick steps Rearray Transfers the contents of a 24 96 or 384 well plate to another 24 96 or 384 well plate by the use of the colony picker pins Order is specified via text file Sample text files are found in C Picker RearraySourceFiles Use Default96 as a template for rearray functions that do NOT use barcode sc
12. s or positions prior to starting All other plate positions are empty Ifa Microl0x is in the system ensure it is primed IfaRSH 4000 sealer is in the system ensure that there is enough sealing tape for the protocol Ifa Liconic is in the system ensure that the instrument has initialized properly and enough room is available for plates If the F stop is installed ensure it is not activated If UV lights are installed ensure the UV lights are switched off 1 3 Protocol Execution Protocols are used to run the full system Protocols generally follovv the same template of load plates run the picker and then unload plates Having selected and loaded the desired protocol the user can click on the Play symbol in the tool bar of the Run Screen to start the procedure circled in the image below When the protocol is executing the Run Screen display will appear similar to the image below SoftLinx V BSF A Be Be DHX O00 4 2 GPS AI _ _ General Protocol Steps Pick to 96 Deep Well Executing o Delay Protocol Run VBA Script o Run Program Egl Send E Mail Modify Variable o End Protocol jaw Parallel Processes C Region OA Conditional Statement Loop Process Pick to 96 Deep Well Expand All Collapse All A xoq oo Initial Load Plates a MovePlate A vvait
13. t plates are moved to the picker Preparation of the source plate Omnitrays and SBS standard plates which have source media are moved to the picker Lids are also removed prior to picking If a user has selected a petri dish as the source manual removal of lids are required The protocol may also have the option to allow the user to swap petri dishes during picking The picker may perform a clean all needles command prior to the first pick Once the initial load of plates has been completed picking or rearraying will commence The Main Process is a repeating section of steps which executes only if plates are available in both the source and target nests The Main Process is as follows Perform the pick or rearray as indicated in the protocol Return the target plate and place a new one if the target plate is full Target plates are relidded if they had a lid Target plates may be sealed by an automated sealer Target plates may be returned to either a stack or a liconic incubator Return the source plate or prompt for new source if it has been fully picked Source plates are relidded if they had a lid Source plates may return to a stack or Repeat the process if the plates were replaced successfully Once the workcell runs out of source or target plates then the system performs a cleanup process as follows Return the last target and source plate Clean the picker The protocol will then exit allowing users to
14. that less water is splashing onto the pin Ensure the target pins are going deep enough into the wells for inoculation Deepwell plates should be at least 70 full to reach wells The location of the place pin when activated can be placed deeper by screwing the black piston to a lower level 17
15. to set up the instruments in your workcell MiNeyiok Fie name 7 Files of type Softlinx Protocol files stp y Cancel At this point the user can click Open Protocol to access protocols for this system Pre developed protocols are available for standard colony picking rearraying and segmented picking Additional protocols are created based on customer requirements but will always follow the same basic protocol template outlined in the manual The selected protocol will be loaded and shown in the main SoftLinx screen At this point the user can load all plates into the proper positions and start the system by pressing the play button Additional information about SoftLinx V can be found in its help file or manual 1 2 Starting a Run Checklist The following items should be checked prior to starting a SoftLinx RapidPick Protocol This list assumes all calibrations and robot positions have been correctly saved All instruments have been turned on Platecrane is on and in a safe position for movement away from the picker The RapidPick software is active and marked as Online The RapidPick camera cap is off and the camera is in position The RapidPick wash bottle is full of clean deionized water The RapidPick trash bottle is empty The RapidPick has the proper imaging parameters necessary to detect the colonies to be picked for this protocol All plates must be in the correct stack
16. ttom of the screen This includes messages such as when a protocol starts or stops when the plate crane gets a plate and when the Picker begins a colony pick or rearray step Details about SoftLinx V can be found within the SoftLinx V Help File 7 1 4 Log Data The RapidPick logs all colonies that have been picked including image of plates and saves them in multiple formats for the user to digest Picker logs can be found in the following locations C Picker Pick Logs C Picker Rearray Logs C Picker Transfer Logs The Pick and Rearray logs are created by the picker software to denote source plate target plate and transfer wells SoftLinx creates the Transfer Logs to include images as well as csv files to show which colony in the image corresponds to the proper target well when picked This data can be accessed in graphical format by entering the SoftLinx RapidPick setup screen which is accessible by selecting Manage Instruments clicking the RapidPick and clicking Instrument Setup A View Picked Colony Data This selection allows the user to view Source Destination relationships between each actual colony picked and the target well it inoculated The user can view the data by either Colony Plate barcode ID or by Target Plate barcode ID An image of the appropriate colony plate is shown with the picked colony locations highlighted in GREEN and a large green circle around the colony that inoculated the well in the row se
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