Colony Counting & Picking

Compatible Labware

• Source plates (agar plates with colonies):
  • Thermo Scientific™ Nunc™ OmniTray™ Single-Well Plate, Catalog number external page 165218
  • Molecular Devices Bioassay QTrays (with or without 48-section divider), Ref. external page #X6023/#X6029
    • The QTrays are only available for manual operation, i.e. QTrays and target plates will have to be placed and remove by the user. This workflow will not be explained here as it will require a separate, specialized training of the user.
• Target plates (well plates containing growth medium):
  • Thermo Scientific™ Nunc™ MicroWell™ 96-Well, Nunclon Delta-Treated, Flat-Bottom Microplate, Catalog number external page 168055
  • Ritter Riplate®SW 2ml 96 Wells (deep-well plate), Article no. external page 43001 – 0020
  • Thermo Scientific™ Nunc™ 384-Well, Non-Treated, Flat-Bottom Microplate, Catalog number external page 242757

Preparation

• Define colony picking parameters (skip if you already defined picking parameters):
  • This part of the workflow will only be done with the help of a member of the LAF or a super-user.

• Fill the wash baths with 70% ethanol, sterile water, and 1% bleach respectively. If the troughs are not on the deck, they were cleaned before and are drying at the sink. Just get them from there. It is okay if they are not fully dry yet.

• Make sure the nests are set up according to the following layout:

1.  Log into the CellarioScheduler with your Cellario credentials (you will get those during the training).

2. Go to the "Order" tab

3. Add a new order selecting the colony picking protocol in your group folder.

4. Choose the appropriate order template and select the number of OmniTray plates that contain your colonies and the number and type of target plates. 

5. Select which plates you will load into which plate hotel. Make sure the plate types are correct. 

NOTE: all plates will have to be lidded and barcoded on the side with the "frosted" surface (e.g. at the column 12-side of a 96-well plate).

6. Set the parameter: number_of_colonies_per_source to the number of colonies that you want to maximally pick per OmniTray plate.

7. Set the parameter: picking_protocol to the picking protocol name that you prepared above.

IMPORTANT: the name has to match exactly.

8. Save the order.

9. Load your plates into the hotel(s) accroding to the layout selected above. Make sure the barcodes are facing you when you load the plates. Note your barcodes/barcode ranges.

10. Go to the "Analyze" tab.

11. Select your order from the list (double check the name and order number) and press "Simulate". This will show you an estimate how long the order will take.

IMPORTANT: If there are any errors here, don't proceed and contact the LAF team.

12. Go to the "Run" tab.

13. Initialize the system if it isn't initialized already. If the play button is visible, it is not initialized. If the pause button is visible, it is initialized.

14. Select your order from the list (double check the name and order number) and press "Start Run".

15. Log out from Cellario to make sure nobody else uses your account to run an order.

Finalize Run

1. Log into the CellarioScheduler with your Cellario credentials
2. Go to the "Run" tab to check whether your order finished.
3. Collect your plates from the plate hotel. Double check that they are your plates by checking the barcodes you noted before. It is possible that another users plate finish their run in the meantime and end in the same plate hotel.
4. Select your order and press "Complete Run" to confirm that your order is finished and the plates were removed. This frees up the hotel positions for other runs. IMPORTANT: only confirm the removal of the plates after you actually removed the plates to avoid crashes!
   
5. Log out from Cellario.

For more information, please visit our wiki.