The Lab: Cultures, Cryo, Plates and Liquid Cultures

The lab pages are under Lab in the sidebar:

• Cultures: your culture library, such as tissue clones, isolations and slants.
• Cryo Inventory: the cultures kept in a freezer (cryo, liquid nitrogen or -80 C), by vial, by strain or by box.
• Agar Plates: plates and their observations.
• Liquid Cultures: syringes, jars and bags of liquid culture.

Each item records the item it was made from, its parent. That chain is its lineage, and it carries on into the grain spawn and blocks made from it.

Who can do what

Item types and stages

Each kind of lab item can have your farm’s own item types, with their own stages, discard reasons, media and places. A Manager sets them up under Configuration > Item types. See Configuration.

• If your farm has item types for a kind, the new-item form shows them as choices at the top, and the item moves through that type’s stages.
• If not, the item uses the standard statuses. Cultures: Active, Depleted (used up), Archived, Contaminated, Discarded. Plates and liquid cultures: Colonizing, Ready, Used, Contaminated, Discarded.

Create a culture

1. Open Cultures and click New Culture.
2. Pick the item type, if your farm has them.
3. Fill in the Name.
4. Pick the Catalog strain if your farm has a strain catalog. It fills in Species and Strain. Otherwise type them.
5. Pick the Source and add Source details if you like, such as the vendor or spore source.
6. Under Parent (optional), pick the culture, plate or liquid culture it came from. Leave it as no parent for a fresh tissue or spore isolation. Generation is set from the parent; with no parent, leave it at 0.
7. Pick the Storage method and fill in Storage location, Location, Tube position and Tube barcode as needed.
8. Click Create Culture.

A culture stored as cryo, in liquid nitrogen or at -80 C also shows on Cryo Inventory.

You can also start from an item’s page: Make from this culture has New plate from this culture, New liquid culture from this culture and New culture from this culture. The parent is filled in for you.

Cryo Inventory

Open Cryo Inventory. Pick a view:

• All vials: every vial on hand. Filter by species and viability. Used-up, archived and contaminated vials are hidden unless you tick the box to show them.
• By strain: one line per strain, oldest vial first.
• By box: each box in the cryo freezer with its slots. Boxes are locations you add inside the freezer under Locations. A box is 9 x 9 unless you set a size on it.

Log a viability check (Manager or Owner)

1. On a vial’s row, click Log Viability Check.
2. Pick Viable, Suspect or Non-Viable.
3. Click Save. The check is dated now.

Discard vials in bulk (Manager or Owner)

1. Click Discard in bulk.
2. Pick vials by Cryo box, Strain or Preserved before. Every one you set must match.
3. Pick the Reason. If it is Other, a Note is required.
4. Click Review N vials, check the list, then click Discard N vials.

Any vial that couldn’t be discarded is listed with the reason when it finishes.

Create agar plates

1. Open Agar Plates and click New Plate.
2. Pick the item type, if your farm has them.
3. Under Parent (optional), pick the culture or plate it was transferred from. You can leave it empty to start a new line, but only for a single plate.
4. Set Number of plates, from 1 to 100.
   • One plate: you can give it a Label.
   • More than one: a parent culture or plate is required. Each plate is named from the parent’s name, the transfer date and a number. Numbering continues past plates that already have those labels.
5. Fill in the Transfer date (required), and Pour date, Media, Vessel, Location, Media recipe and Additives as needed.
6. Click Create Plate (or Create N Plates).

Plating from a freezer vial

When the parent is a frozen vial:

• Grains used shows how many grains or aliquots the plates take from the vial.
• Mark the vial used up sets the vial to Depleted once the plates are saved, so it leaves freezer stock.
• Thaw a vial makes one petri and one slant from the vial and marks the vial used, in one step. The button reads Thaw and Plate.

Log a plate observation

Workers, Managers and Owners log observations.

1. Open the plate and click Log Observation.
2. Set the Date, slide Growth %, and add Morphology Notes.
3. Pick a Score, if your farm has plate scores.
4. Tick Flag contamination if you see it.
5. Click Log.

The plate’s Colonization follows the newest observation by date, so a back-dated observation doesn’t overwrite a later one. Its Score follows the newest observation that gave one.

Plate scores

Plate scores are your farm’s own words for grading a plate. A Manager adds them under Configuration > Enumerables, in the Plate scores list. With no scores set up, the observation has no Score field.

Purity and contamination

Purity Assessment on the plate shows Contaminated once an observation flags contamination.

Flagging contamination, in an observation or by choosing Contaminated, follows your farm’s contamination setting under Configuration > Lifecycle:

• Discard right away: the plate is ended in the same step.
• Keep it and monitor: the plate stays where it is with a contamination flag, until someone discards it.

On a contaminated item’s page, the Make from this … card says to start from a clean item instead.

Create a liquid culture

1. Open Liquid Cultures and click New LC.
2. Under Inoculated from (optional), pick the plate, culture or liquid culture, or leave it empty to start a new line (for example, a purchased syringe).
3. Fill in the Vessel, Volume (ml), Media and Inoculation date. These are required.
4. Optionally set Units available, Location and Visual notes.
5. Click Create LC.

From a liquid culture’s page, Make from this liquid culture has New liquid culture from this LC and New grain spawn batch from this LC.

Units left

A liquid culture can keep a count of syringes left, under Units available. A culture can keep a count under Grains or aliquots left. Workers can change the count. Leave it empty to stop counting.

A Manager can set Flag an LC low at under Configuration > Lifecycle > Lab rules. A liquid culture at or below that count shows Low.

Change the stage or status (Manager or Owner)

1. Open the item.
2. In the Status card, pick from Change stage (or Change status if the item has no item type). Stages that end the item are listed under Ends it.
3. If you pick Contaminated, say what you saw.
4. Answer the QC check if the stage you are leaving has one. See QC Checkpoints and Release.
5. Click Save stage (or Save status).

If your farm turned on Lab next stages, an item can move only to the next stages its item type lists, or forward. Discard works from any stage. See Optional Features.

If a stage has a planned length, the item shows on Due today when it is due to move on. See Stage Schedules and Due Today.

Moving an item to another place

A Manager changes an item’s Location with Edit. On the floor, a scan station also moves cultures, plates and liquid cultures by scan. See Scanning on the Floor.

Notes, discards and contamination reports

Every item page has a Notes and losses card with its history.

• Add a note: type it and click Add note.
• Discard: click Discard, pick why it is being discarded, and click Discard. If the reason is Other, say what happened. It is marked discarded and the reason goes into its history.
• Report contamination: in a stage marked Released by a Manager, a Worker sees Report contamination instead of Discard. Pick What did you see? and click Report. The item is flagged and stays where it is. A Manager has to end it.

Parents, lineage and suspect sources

• Each item page shows its parent. Click View Lineage for the whole chain, or View in Sporeline to browse it.
• A Manager can mark an item as a suspect source in the Suspect source card: fill in Why is this source suspect? and click Flag as suspect. Everything made from it, now or later, shows a warning. Clear flag removes it.
• Recall from this item (Manager or Owner) opens the recall scope for the item. See Traceability and Recall.

Print a lab label

1. Open the culture, plate or liquid culture.
2. Click Print label.
3. Pick the Tag size. It is for this print only.
4. Click Print. The label opens in a new tab for your printer’s print dialog.

If your browser blocks the new tab, click Open label. For printers and templates, see Label Printing.

With an AI assistant

If you’ve connected an AI assistant, you can ask it to add a note or throw out a lab item for you. Notes and discards from an assistant follow the same rules as the buttons on the item page, and Workers, Managers and Owners can use them.

• Add a note: say something like “note on plate P-12 that the lid cracked.” The assistant uses lab_item_note, shows you the plate and the note first, and adds it once you say yes. The note lands in the item’s Notes and losses history like one you typed.
• Discard: say which item and why, for example “throw out LC 14, it’s contaminated.” The assistant uses lab_item_discard and shows you the item, its status, the reason and how many items were made from it before anything changes. Once you confirm, it’s marked discarded, the loss is logged and the reason goes into its history. Items made from it stay as they are and still trace back to it.

The assistant should always ask you for the reason rather than guess one. If the item sits in a stage that a Manager releases, a Worker’s contamination discard is saved as a contamination report instead, the same as Report contamination on the page. If your farm has Approve every AI change turned on, the change waits on the approvals page until someone approves it.

When something goes wrong

• “Only a Manager or Owner can record new plates.” — ask a Manager or Owner. You can still log observations on existing plates.
• No New Culture, New Plate or New LC button — your role can’t create lab items.
• “Couldn’t load your item types.” — the create button waits until they load. Click Retry.
• “Several plates at once need a parent.” — pick the culture or plate they came from, or make one plate with no parent.
• “Number of plates must be a whole number from 1 to 100.” — make 100 now and the rest in a second batch.
• “Flagged contaminated — start from a clean item.” — pick a clean parent instead.
• “Say what you saw before marking it contaminated.” — fill in the note, then save.
• “That is already its stage.” — pick a different stage to change it.
• “Say why before flagging it.” — fill in why the source is suspect.
• “Enter a whole number up to 10000, or leave it empty to stop counting.” — fix the count.
• “Couldn’t load the farm’s plate scores” — the observation can still be logged, without a score.
• Status card missing — only Managers and Owners change stages. Workers can add notes, discard or report contamination.

With an AI assistant

If you have connected an AI assistant (see Connect an AI Assistant), you can ask it how full your cryo boxes are, such as “which box has room for six more vials”. It reads them with cryo_box_list, which lists each box in a freezer, dewar or tank with its size, the vials on hand, the vials that still need a slot and the free slots, counted the same way as the By box view of Cryo Inventory. Everyone on the team can ask, as in the app.