Plate imaging, strains, and sequences in one microbiology workspace
The colony count, the strain it came from, the freezer box it lives in, and the sequence that identifies it are four records in four tools. Conspecta keeps them as one.
The microbiology bench, in one browser tab
One project. Every plate image, count, and sequence stays linked to the strain behind it, and that strain carries its passage number, growth conditions, and freezer location.
Imaging
Object detection, area coverage, and intensity measurement on LIF, TIFF, and PNG in the browser, with every image attached to the strain and the plate it was taken from.
How most labs do it today. Images land in a dated folder on the computer that took them. The number that matters ends up in a spreadsheet with no way back to the image it came from.
Counting
Open a plate image and the detector counts every colony, with no threshold to tune. The setup stays with the analysis and re-runs across the whole series, with the parameters stored beside the count.
How most labs do it today. The macro's thresholds live in a script rather than with the counts they produced, so repeating the assay next year means re-deriving them first.
Biofilms
Coverage, area, and intensity measured the same way across the series, on flat images and on confocal z-stacks, with the settings saved alongside the result.
How most labs do it today. A hand-traced region is slow to produce and isn't saved with the number it produced, so repeating the measurement starts from scratch.
Strains
Strains and isolates are samples with structured metadata, and every image, sequence, and result that came from one stays attached to it.
How most labs do it today. Passage number, growth conditions, and resistance markers drift between personal copies of the sheet until no version is authoritative.
Freezers
Map freezers, shelves, and boxes, and give every strain a location that travels with its record.
How most labs do it today. A box gets moved and the sheet doesn't follow, so the record and the freezer drift apart.
Sequences
BLAST, alignment, phylogenetics, and restriction analysis, all attached to the strain the sequence identifies.
How most labs do it today. The sequence that identifies an isolate lives in a different app from the isolate, so the physical tube and its identity are only linked by a filename.
Amplicon
Import the abundance table as CSV or TSV into a data table beside the samples it came from, and read the tree into the phylogenetics viewer as Newick. Conspecta analyzes pipeline output and does not run the pipeline.
How most labs do it today. The pipeline finishes and its abundance table and tree sit on a cluster path. Weeks later a figure gets made in R, disconnected from the samples that produced it.
Figures
Charts are built from the counts themselves, and notes, protocols, and multi-panel figures live in the same project as the plates.
How most labs do it today. Counts are pasted into a stats package and the plot into a figure, so the finished panel has no route back to the plates behind it.
See it on your own plates
Upload a plate photo and get the count back in minutes. Nothing to install, and the count stays with the image it was measured from.