File Formats and Importing

Conspecta reads the formats your instruments already produce. This page lists what each workspace opens, what it writes, and the formats it doesn't handle today.

What Conspecta Opens

Import is under the ⋯ in the workspace header, wherever a workspace can take a file. Some workspaces also offer it as a tile beside the blank option when you create a note, a data table, or a panel.

A drag works in three places:

• Notes and imaging take a drag onto the list at any time, in the workspace or inside a folder, and anything the workspace cannot read is named back to you rather than passed over.
• Elsewhere an empty workspace takes a drag onto the page.
• A figure takes one onto an empty panel slot.

Whichever route you take, a CSV lands on a column-mapping step first, where Conspecta shows the column it matched each field to and lets you repoint any of them. That step maps one file at a time, so a drag carrying several starts with the first and names it, and the others go in one after.

Locations are the one import that arrives flat, so you set what sits inside what afterwards.

An order's receipt is an attachment with a list of its own. It takes a PDF or a photo (.png, .jpg, .webp, .heic), up to 25 MB.

A figure panel takes a picture or a PDF, and a PDF arrives as its first page rasterized to a PNG, so what sits in the panel is an image. A chart's numbers come from a data table or from a file imported in the chart editor, which reads the same formats Data Tables does.

A microbiome table imports from either place. BIOM 1.0 (.biom) and QIIME2 visualizations (.qzv) both arrive with a column per taxon and a row per sample, with the sample IDs labeling the rows down the left of the table. A QIIME2 taxa bar plot comes in at the most detailed level the file carries.

A table holds up to 512 columns. A raw feature-level BIOM file is usually far wider than that, and importing one stops with its column count named, so collapse it to a higher taxonomic level first.

Images dropped into the body of a note are a separate list. PNG and JPEG go in as they are, and a TIFF is converted to a PNG of its first page.

Opening a LIF File

A Leica Image File (.lif) holds a whole session: several series, each with its own z-slices, channels, timepoints, and tiles. Conspecta reads it in your browser, so a multi-gigabyte acquisition uploads with no conversion step.

Every series becomes an image you can open, with its slices, channels, and channel names intact, which makes colocalization and marker classification possible. The pixel size the microscope recorded comes with it, so scale bars, rulers, and area measurements on those series read in microns. The .lif file itself isn't stored, because every series inside it is kept as an image.

The limits are 5 GB per LIF, 100 MB per ordinary image, and 200 files per upload. Keep the tab open while a large upload runs, because closing it cancels what's left.

Opening an FCS File

Conspecta supports FCS 3.0, 3.1, and 3.2. An FCS 2.0 file still opens, but some of its legacy encodings can be misread, so Conspecta flags it when you upload one. Parameters, keywords, cytometer name, acquisition date, tube and well identifiers, and any embedded spillover matrix all come across, so an analysis can offer to apply the cytometer's own compensation.

Files stored with ASCII rather than binary data aren't supported.

A gated population exports as an FCS file, with the gate's name written into the file's keywords, so you can open the population in other flow software.

A FlowJo 10 .wsp or a Gating-ML 2.0 gating file is read entirely in your browser, up to 64 MB, and stays on your machine while you look at what it holds. The Upload files dialog takes one as well as FCS files, and opens its gating import rather than treating it as data. Gates that can't be rebuilt are named on screen with the reason. Gating files and templates covers what carries over in each direction.

Sequence Files

FASTA and GenBank both import, several files and several records at a time. A GenBank record brings its annotations and its topology, so a circular plasmid opens as a plasmid map.

You can skip files entirely and fetch by accession from NCBI or UniProt, or paste a sequence and let Conspecta detect whether it's DNA, RNA, or protein.

A SnapGene .dna file imports as it is, keeping its features and its topology, so a plasmid opens as a plasmid map. A .dna records no title of its own, so the sequence takes the filename, which you can rename afterwards.

A Sanger trace .ab1 imports as a sequence, taking the sample name the sequencing order carried and recording the instrument and the run date in its description. Its per-base quality comes across with it. To line several reads up against the sequence you had made and look at the peaks, open that sequence and use Sanger Alignment, described in Checking a sequence against Sanger reads.

Formats to export around today: EMBL, FASTQ, and GFF3. Export the sequence as GenBank or FASTA from the tool that made it, and that will import cleanly.

Spreadsheets

Data Tables import CSV, TSV, and Excel, one table per file, named from the filename.

Excel formulas come across. Conspecta recomputes the functions it supports and keeps the rest as written, each with the value it had in Excel. A banner on the table explains which happened.

For samples and inventory, a CSV import matches column headers loosely, including the header names other lab tools export, so a spreadsheet from elsewhere usually maps without editing.

Formats Conspecta Doesn't Read

• Microscopy: .czi (Zeiss), .nd2 (Nikon), OME-TIFF, and whole-slide formats (.svs, .ndpi, .mrxs, .vsi, .scn) are not supported. Export to TIFF from your acquisition software.
• Sequences: EMBL, FASTQ, and GFF3. Export as GenBank or FASTA instead.
• Video: .mov and .avi are refused. Re-encode to MP4 or WebM.
• Gating: FlowJo 9 and earlier wrote a different workspace layout, and Gating-ML 1.5 a different standard. Both are refused with the format named, so re-save from FlowJo 10 or export Gating-ML 2.0.
• Office: the pre-2007 binary .doc and .xls are not read. Re-save the file as .docx or .xlsx before you import it.

What Conspecta Writes

Your data leaves in formats other tools read:

Anything that comes out as an Excel workbook can come out as CSV instead, with the same numbers as plain text, one file per sheet, zipped when a workbook has more than one.

Exports are free and never count against compute usage. Share and export covers the whole-project backup.