Image analysis, samples, and figures in one cell biology workspace
A cell biology experiment ends as a number in a figure. Conspecta keeps the image, the measurement it produced, the dish it came from, and the figure it lands in inside a single project.
The cell biology bench, in one browser tab
One project. Every image, measurement, and figure stays linked to the dish, passage, treatment, and timepoint behind it.
Import
Upload LIF, TIFF, PNG, and JPEG into the project your samples already live in, and they open in the browser on a Mac, a Chromebook, or a managed university laptop, with nothing to install. Conspecta starts after acquisition and does not drive the microscope.
How most labs do it today. The scope computer in the core exports a LIF or a folder of TIFFs, and the data leaves on a USB stick or a share named after a date. The LIF then opens on the one machine where Bio-Formats and the right Java version are configured, and not on the student's laptop or a locked-down campus machine with no admin rights.
Counting
Open an image and a segmentation model counts every cell, with no threshold to tune. The same detector runs across the whole set, and the settings behind a count are stored with it.
How most labs do it today. A threshold gets nudged image by image to cope with bright and dim fields, and the value that produced any given count isn't stored with the count. The macro lives in one person's home directory.
Measurement
Area coverage (confluency, wound healing, staining), per-cell marker intensity across channels, marker-positive fraction, per-object shape, and colocalization with Pearson's, Manders', and Costes thresholding, each still attached to the image it came from.
How most labs do it today. Numbers land in a Results window, get copied into Excel, and lose every trace of which image and which channel produced them.
Plots
Measurements feed charts directly. Re-run a detection and the numbers downstream follow it instead of going quietly out of date.
How most labs do it today. Re-running the analysis means a fresh export and a fresh paste, and the bar chart keeps no record of which measurement produced it.
Cultures
Every image links to the sample it was taken from, and that sample carries its passage, treatment, and timepoint into every measurement and plot built from it.
How most labs do it today. Which folder was passage 12, siRNA knockdown, 48 hours? The answer is a filename convention, right up until someone renames a folder.
Writing
Notes, image analysis, and multi-panel figures sit in one project, with panel labels exported together, and the figure is built from the analysis rather than pasted next to it.
How most labs do it today. The notebook describes the analysis in prose. The figure is a screenshot of a measurement that has since been re-run twice.
See it on your own plate
Upload one image set and run a detection. The counts come back attached to the images they were measured from, not in a separate spreadsheet.