Track Your Samples

The Samples workspace is the register of every specimen in a project: cell cultures, tissue, microbial isolates, environmental samples, plates. It records what each one is, where it's stored, what state it's in, and what it's been through, so a tube in a freezer can always be traced back to where it came from and forward to the results it produced.

Registering a Sample

New sample asks two things. First, what kind of sample it is, from a grid grouped into Common, Organisms, Microbial, and Derived & Environmental. Then a name, and whether it's private to you or shared with the project.

That's the whole creation step. Everything else is filled in on the sample itself, where every field saves as you type. There is no save button, and no long form standing between you and a registered sample.

Sample Types

The type you pick decides what the sample can record. A cell culture wants passage number and mycoplasma status, a bacterial isolate wants a biosafety level and an antibiotic resistance profile, and a mouse wants a genotype and a treatment group. Rather than one form with ninety fields, each type asks only for what it needs.

Common

Organisms

Microbial

Derived & Environmental

Every type also carries the shared fields: name, external ID, description, tags, status, storage location, expiry, and how it was collected.

Why the Type Matters

The fields are the visible half. The type also changes what the sample can do.

Organism and Plant samples get a Health tab, and open on it rather than on Connections. Record an observation and you capture a health status, a health score, and photos in one step. The photos upload as you add them, with the same progress and thumbnails you get on the Images tab, so Cancel drops the reading you were typing and leaves the photos on the sample. The tab then plots the score over time and tells you how it has moved since last week, so a cohort that's declining shows up as a line rather than as a hunch. The photos attached to an observation are ordinary sample images, which means you can run image analysis across them and get numbers out of a fortnight of photographs.

Cell Culture samples keep a bench log, and open on the Activity tab that holds it. Log action records what you did at the bench: Feed, Split, Observe, Thaw, Freeze, Mycoplasma test, or Discard, each with one or two fields. An action that implies a field change makes it for you, so the sample stays true as a by-product of logging. A split moves the passage number up one and clears the confluence, a thaw sets the passage and marks the sample active, a definitive mycoplasma result sets the mycoplasma status, and a discard marks it disposed. The time on an entry defaults to now and can be moved back with the quick choices or the date picker, because logging usually happens after you leave the hood. Fields remember your last entry of the same kind, so a routine feed opens with the media and volume you used last time already filled in, and Log & add another saves the entry and returns you to the picker for the next one.

An Observe entry captures the look under the scope: photos, confluence, contamination, and Appearance, all optional. Appearance is a row of chips covering what you see down the scope, from Normal, Clumped, and Overgrown through Detaching, Floaters, and Medium cloudy, and you tap as many as apply so one entry records the whole picture. The photos land on the Images tab too, and a contamination flag shows red on the log where the whole team sees it. Back on the workspace, the sample's card shows the latest entry next to its passage, so "Fed 2 days ago" is readable without opening anything. Correct an entry with the pencil or delete it with the trash, and either one also undoes what the entry wrote to the sample, wherever those fields still hold that value. You can correct or delete the entries you logged, and the project owner can do either on anyone's. Every entry, correction, and deletion is kept permanently.

Entries sit on the Activity tab alongside the sample's edits, comments, and sign-offs, in one timeline ordered by when each thing happened. An entry you backdate sorts under the time you did the work, so a feed logged at lunch for a morning job lands where it belongs. Once the timeline has a few events, a filter above it splits the view: Bench is what you logged, Changes is what was edited on the record itself.

Microbiome samples unlock the QIIME2 export. A project containing at least one gets an Export QIIME2 button, producing the metadata .tsv that a QIIME2 pipeline expects, built from the fields you already filled in.

Extract samples carry their own quality control. A260/A280 and RIN sit next to the concentration, so the sample itself says whether it was good enough to sequence, and you can filter or group by that later.

Microorganism, Virus, and Fungi samples record a biosafety level, which you can filter and group the whole workspace by. That makes "what BSL-2 material do we have, and where is it" a question with an answer.

Importing a Batch

Import takes a CSV or TSV. Set a default sample type for the whole file, and optionally drop everything you're importing straight into a group. Column headers are matched loosely, including the header names other lab tools export, so a spreadsheet from elsewhere usually maps without editing. Name is the only required column. External ID, description, status, collection details, species, strain, cell line, tissue type, notes, and tags are all recognized.

You can also drag a .csv or .tsv straight onto an empty workspace.

The Sample Profile

The sidebar holds the sample's identity: its status, name, external ID, description, storage location, expiry date, tags, the fields specific to its type, and how it was collected. All of it edits in place.

Status tracks where the sample is in its life:

Across the top, a Cell Culture sample leads with Log action, which opens the bench-log composer from whichever tab you're on. The ⋮ menu beside it holds the rest: Run protocol starts a protocol run against this sample, Print label produces a scannable label, and Share with project or Make private switches who can see it — the sample's creator only. A private sample says so in the sidebar too: a Visibility row reading Private to you, which opens the same choice. It appears only while the sample is private.

The rest of the profile is in tabs.

Connections is the sample's map. A graph shows where it came from and what came out of it, running through photos, image analysis, cytometry, data tables, figures, protocol runs, notebook pages, inventory, orders, and tasks. Set parent sample records where it came from, and reads Change parent sample once it has one. Link on the map connects the sample to anything else you search for in the project, such as an analysis, a figure, a task, or a protocol run, and the new connection appears on the map right away. Pick another sample from Link and it asks which of the two came first, so you can name a sub-sample while standing on the one it was taken from. Below the graph, linked analysis and figures are listed, and Image analysis starts one from this sample's photos. Any FCS files attached to the sample are listed there too, and once it has at least one, Flow analysis appears beside it and opens a cytometry analysis over them. See Analyze Flow Cytometry Data for how files get attached in the first place.

Images holds the sample's photos. Drag files anywhere onto it, or use Add photos. Dropping photos on the tile at the top of the sidebar does the same thing from whichever tab you're on, and opens Images so you can watch them arrive. A batch uploads in place: each photo holds a spot in the grid while it transfers, Cancel stops one mid-transfer, and the count next to the heading tracks the whole batch. A photo that fails keeps its spot with the reason and a Retry; a file that isn't a photo Conspecta can store says so and offers Dismiss instead. Microscopy TIFFs get a preview like anything else. To remove photos, tick the checkbox on one to start selecting — Select all takes every photo currently loaded, Select none clears them without leaving, and Delete removes what you picked.

Activity is the sample's whole history in one timeline: every change to the record, and on a shared sample in a team project the comments, @ mentions, and sign-offs as well. On a Cell Culture sample it also holds the bench log, which Log action across the top of the sample writes to. Follow a sample from here to get told when it changes.

Health appears on Organism and Plant samples, and those two open on it. Cell Culture samples open on Activity, where their bench log lives. See Why the type matters above.

Expiry

Give a sample an expiry date and Conspecta watches it for you. Once the date passes, an Active or In Use sample flips to Expired automatically, both when the date is set and on a nightly sweep.

Two things about that are worth knowing. Samples already marked Consumed, Disposed, Lost, or Archived are left alone, because those are final states and being past a date doesn't change them. And on the same save, the date wins over a status you set by hand: putting a past-due sample back to Active won't stick unless you push the date out too.

The Expiring soon button gives you everything expiring in the next 30 days or already past, soonest first, across every folder rather than just the ones you've scrolled through.

Organizing

Group by reorganizes the workspace by location, species, strain, type, status, health, growth stage, life stage, biosafety level, or the month a sample was created, and remembers your choice. Filter narrows by those same dimensions, and by whether a sample is starred or has photos. The box in the toolbar matches names, species, strains, external IDs, and tags.

Folders group samples by experiment or batch. A folder has to be empty before it can be deleted, so nothing disappears with it.

Select several samples for the bulk bar: Move them into a folder or another project, Share or Make private, Group them, Analyze images across all of them at once, Print labels, or Delete.

Moving samples to another project takes their photos along, and the original owner stays the owner. See Moving work between projects.

Large workspaces load 500 samples at a time with a Load more at the bottom. Search and Expiring soon reach past that.

Sample Groups

The Groups tab is the second way to organize samples, and it answers a different question. Folders are where a sample is filed. A group is what a sample is part of: a study, a cohort, a batch, or a control group.

New group takes a name, a type, and whether it's private or shared. Inside, each member carries a role of Sample, Control, Calibration, or Blank, so the analysis knows which is which. A sample can belong to several groups at once.

From a group you can Add samples, change roles in bulk, run image analysis across every member, or Run protocol once against the whole group, which creates a single run linked to all of them. Add samples opens your sample list with the current members already ticked, so unticking one removes it from the group in the same dialog box.

Deleting a group never deletes its samples. It removes the grouping and nothing else, and the dialog box says so before you confirm.

Well Plates

Creating a Well plate sample opens a plate workspace rather than the usual profile: a well map you lay out, prep, run, and read. It has its own page, Well plates.

Templates in the workspace header lists every plate layout the project has saved, at any plate size, and is where you rename or delete one. See Templates.

Labels and Scanning

Print label on a sample, or Print labels on a selection, produces sheets of QR labels. Choose the label stock (Avery 5160, Avery 5167, Avery L7160 for A4, or an 89 × 28 mm roll), how many copies of each, and which position on the sheet to start at so a part-used sheet isn't wasted. Then Download PDF or print directly.

Scanning works from anywhere in the app. With a handheld scanner connected, scan a label in any workspace and Conspecta opens that sample, item, or location, and a Scan ready chip tells you it's listening. On a phone, use the Scan tile to do the same with the camera.

If a scanned code isn't linked to anything, you're offered Link to a sample or Link to an item right there, which is how you adopt a box of pre-barcoded tubes: scan, pick the sample, scan the next. Scan to set ID on a sample profile does the same in reverse, reading a code into that sample's external ID.

The label encodes only the sample's identifier, with no address in it, which is why a label keeps working after the sample is moved to another project.

Exporting

Samples in a project containing microbiome samples get an Export QIIME2 button, producing a QIIME2 metadata .tsv of the current folder plus your starred samples. For everything else, the full sample export lives in Settings → Export, which produces an Excel workbook of the whole workspace. See Share and export.