Genetix ClonePix FL Manual

ClonePixTM FL
Quick Set-Up Instructions
Software Release: 1.2.13.971
07MAN1055.A2
Effective Date: 01-Jun-10

GENETIX > CLONEPIX FL QUICK INSTRUCTIONS > CONTENTS
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Contents
What are Quick Set Up Instructions?...............................................................3
Starting up ClonePix FL ....................................................................................3
Loading plates....................................................................................................4
Preparing for a Pick Run ...................................................................................5
The Pick Run ......................................................................................................6
Imaging Settings.................................................................................................................... 7
Picking Settings ..................................................................................................................... 8
Sanitize Pin Options .............................................................................................................. 9
Start Pick Run........................................................................................................................ 9
Preview................................................................................................................................ 10
Select Wells......................................................................................................................... 12
Summary ............................................................................................................................. 12
Imaging................................................................................................................................ 12
Results................................................................................................................................. 12
Select Groups...................................................................................................................... 13
Picking ................................................................................................................................. 14
Finish ................................................................................................................................... 14
Powering down ClonePix FL...........................................................................14
Contact Details.................................................................................................15

GENETIX > CLONEPIX FL QUICK INSTRUCTIONS > WHAT ARE QUICK SET-UP INSTRUCTIONS?
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What are Quick Set-Up Instructions?
These instructions are designed to enable a new user to undertake a simple picking run on
ClonePix™ FL. The following instructions offer guidelines only. No attempt should be made to
use ClonePix FL before the system has been fully installed by a Genetix Approved Engineer.
For full information please read the ClonePix FL Robot Manual and Software Applications
Manual. Please refer to the Genetix website for the latest reagents & supplies, replacement
parts and optional extras www.genetix.com
Starting up ClonePix FL
• Ensure robot and compressor are plugged in.
• Ensure compressed air gauge is set to 80 psi (5.5 bar).
• Ensure Emergency Stop button is not pressed in.
• Switch on ClonePix FL. The HEPA filtration system works all the time that ClonePix FL is on.
• Press Reset button at the front of ClonePix FL.
• Initiate ClonePix FL software.
• Wipe out ClonePix FL bed with 70% ethanol or fresh Genetix Sterilizing Agent (K8080)
using lint-free cloth.
• Fill the ethanol feed bottle with 70% ethanol and empty the ethanol waste bottle.
• Make sure that the correct Picking Pins are installed for the type of cells to be picked.
o F1 Picking Pins (400µm internal diameter; X4961) for suspension cell picking from
semi-solid medium.
o F2 Picking Pins (700µm internal diameter; X4962) for adherent cell picking from
liquid medium.
Picking Pins should be cleaned by sonication in aQuClean (K2505) and autoclaved. It is
advisable to autoclave the Picking Pin Removal Key (X4948) at the same time. See
General Maintenance section of the Robot Manual for instructions.
If the Picking Pins need to be changed remove the Picking Head and swap the pins. To
do this, click on the Picking Head Management icon, then the Replace Head icon and
follow the on-screen instructions. Refer to the General Maintenance section of the Robot
Manual for guidance on how to remove and replace the head and the pins.

GENETIX > CLONEPIX FL QUICK INSTRUCTIONS > LOADING PLATES
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Loading plates
It is important to know how to load plates into ClonePix FL correctly.
A ClonePix FL bed layout is as shown below.
The Source plate stacker system is located at the rear of the machine, and the Destination
plate stacker system is at the front. Both the Source and Destination stackers have 1
removable Feed cassette (left hand side) and 1 removable Return cassette (right hand side).
Each cassette can accommodate up to 10 standard microplates or 12 Genetix microplates. The
plates are fed individually from the Feed cassette onto the bed, with automatic lid removal as the
plate passes the Return cassette position. On completion of colony picking, the de-lidded plate is
then transferred to the Return cassette where the lid is replaced.
Important notes:
• Plates loaded into a Feed cassette must be of the same type and must match the plate type
selected by the user in the software. Loading of a plate type different from that selected in
the software is likely to damage the plate and the instrument.
• When the Return cassettes are placed in the source and destination stackers, they must be
held firmly in place by use of the Return cassette locking bolt on the right hand side of the
stacker systems. Failure to lock down a Return cassette will cause a malfunction in the
return of the microplates.
• Source and destination plates must be loaded into the Feed cassettes with lids on and well
A1 in the front right-hand corner as shown below:

GENETIX > CLONEPIX FL QUICK INSTRUCTIONS > PREPARING FOR A PICK RUN
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Orientation of source plates in ClonePix FL
Orientation of destination plates in ClonePix FL
Preparing for a Pick Run
Prior to carrying out a picking run, it is important to make sure that ClonePix FL is set up
correctly. The Prepare for Pick Run process is designed for this purpose. This process helps
the user to validate that 1) the pins are firing correctly, 2) the camera, pins and microplates are
aligned, and 3) the fluid system is sterile and ready for use.
• Click on the Prepare for Pick Run icon and follow the on-screen instructions.
When asked to load a source plate, it is recommended that you use a blank Genetix PetriWell-6
plate. However, the use of any configured plate (those present in the drop-down list) should
work. Once aligned using a configured plate type, ClonePix FL is then ready for use with any
configured plate type.
The Prepare for Pick Run process does not need to be carried out prior to every picking run. It
must be carried out every time that ClonePix FL is first powered up.
• Click Close Process to return to the Main Menu.

GENETIX > CLONEPIX FL QUICK INSTRUCTIONS > THE PICK RUN
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The Pick Run
The Pick Run process is designed to aid new users through their first picking run. Use of the
default parameters provided should facilitate successful imaging, colony selection and picking.
The description below assumes that you have plates of cell colonies with fluorescent halos of
secreted protein.
• Click on the Pick Run icon to open the following screen:
The settings can be edited by clicking once on the green section headings.

GENETIX > CLONEPIX FL QUICK INSTRUCTIONS > THE PICK RUN
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Imaging Settings
• Click on the Imaging Settings title to open the following screen:
Fill in the following information:
• Run Annotation
Enter a name to identify this run.
• Source Well Plates
Enter the source plate type that you will use for this run.
• Barcode Options
- Select Read Barcode.
- Select Auto-assign barcode in case of failure.
If you don’t have barcodes on your plates, ClonePix FL will automatically assign a code.
• Batch plates
Select this option. This assumes that you are loading multiple plates that contain the same
sample and that you want them to be processed as a single experiment.
• Source Plate Options
Select Finish when cassette is empty.
• Acquisition Options
This option enables you to choose the images that you wish to capture. If you see
appropriate Image Acquisition options select them here. If not, the acquisition options can

GENETIX > CLONEPIX FL QUICK INSTRUCTIONS > THE PICK RUN
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be created later in Preview (see below). Most users select one white light and one
fluorescent option.
• Prime Probe
The Prime Probe is the acquisition option to be used for colony detection. Select the white
light option if available.
• Review Colony Selection
Select Batch – Review All.
• Click Apply.
Picking Settings
• Click on the Picking Settings title to open the following screen:

GENETIX > CLONEPIX FL QUICK INSTRUCTIONS > THE PICK RUN
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Fill in the following information:
• Destination Well Plates
Enter the plate type that you will use for this run.
• Destination Well Plates
Specify the wells into which you want to deposit. Right click on the mouse to select wells,
and left click to de-select wells. All destination plates will be filled using this template.
• Barcode Options
- Select Read Barcode.
- Select Auto-assign barcode in case of failure.
If you don’t have barcodes on your plates, ClonePix FL will automatically assign a code.
• Deposit Options
- Select Match Destination Plate to Source Plate if you want to start a new destination
plate each time a new source plate is fed in.
• Destination Plate Options
Select Finish when cassette is empty.
• Pick Number Options
Leave as default = Organise by Plate.
• Pin Options
- Select the type of colonies that you wish to pick: suspension or adherent.
- Pick Height Adjustment: Leave as default.
- Aspirate Volume: Leave as default = 5µl.
- Dispense Volume: Leave as default = 7µl.
• Dispersal Options
- Use dispersal: Select if you want to spread out colony cells after picking.
- Dispersal cycles: Use 3-6 for CHO cells and 6-10 for hybridomas.
- Dispersal volume: Leave as default = 20µl.
• Pick Progress Options
- Leave as default = unselected.
• Click Apply.
Sanitize Pin Options
Leave as default – no changes required.
Start Pick Run
• Click Start to begin the Process.
• When prompted, load your cell colony plates into the Source Feed cassette.

GENETIX > CLONEPIX FL QUICK INSTRUCTIONS > THE PICK RUN
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Preview
This is where you set up your Image Acquisition and Colony Detection settings. The screen
should look like this:
Step 1: Set up Image Acquisition settings
• Click on the Acquisition tab.
• If the My Configurations box is only populated with
Default (see screenshot on right), you will need to set
up white light and fluorescent Image Acquisition
options.
• Click New and then click Edit. The following settings
should work for most scenarios:
Description White Light FITC 1s
Excitation Filter WHITELIGHT (TRANS) EGFP/FITC
Exp. Time (ms) 150 1000
LED Intensity 3 128
Camera Focus 2200 2200
Display Color White Green
• Click Save to store each option.