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Confocal analysis, tissue tracking, and figures in one neuroscience workspace

A neuroscience result is a count, an intensity, or a colocalization, traced back to an animal and a brain region. Conspecta keeps the z-stack, the measurement, the section it came from, and the figure it ends up in inside a single project.

The neuroscience imaging bench, in one browser tab

  1. Import

    Upload LIF, TIFF, PNG, and JPEG into the project the tissue already lives in, so a two-week imaging run is in one place the day it comes off the rig, open to everyone on the project. Conspecta starts after acquisition and does not drive the scope.

  2. Z-stacks

    Multi-channel z-stacks open directly in the browser, with independent brightness and pseudocolor per channel, plane-by-plane browsing, and maximum intensity, average, or sum projections. A sixty-plane, four-channel stack opens the same way on a student's managed laptop as on the rig workstation.

  3. Counting

    Open a stack and a segmentation model counts every neuron, with no threshold to tune. Bright and dim sections run through the same detector, the settings behind a count stay with the count, and you count on the projection you're viewing or per plane across the stack for a depth profile.

  4. Colocalization

    Pearson's correlation, Manders' coefficients, and Costes thresholding, plus per-cell marker intensity across channels with positive and negative classification. Every measurement names the section, the channel pair, and the animal it came from.

  5. Plots

    Measurements feed charts directly, grouped by animal, region, and condition. Re-run a detection and the numbers downstream follow it, and each plot still names the measurement it was built from.

  6. Animals

    Track animals, brain regions, sections, and injection sites as samples, so animal 7, contralateral hemisphere, third section from the injection site is a set of fields you filter on. Every image and measurement stays linked to the tissue it came from.

  7. Writing

    Notes, image analysis, and multi-panel figures sit in one project, with panel labels. An entry points at the quantification it describes, so re-running that analysis reaches the panel in the figure.

See each workspace

Image analysisTurn microscopy into numbers you can trust.SamplesWhere it came from, and what came of it.FiguresAdd a replicate and the figure redraws.NotesThe notebook that links to everything else.

Questions neuroscience labs ask

Can I count neurons and puncta without writing a macro?

Yes. Answer a couple of questions about what you are looking at and Conspecta assembles the detection, with no threshold to nudge between a bright section and a dim one. Count on the projection you are viewing, or per plane across the stack for a depth profile. The same detection runs across every section in the set, and the settings behind a count are stored with the count.

Can I work with confocal z-stacks in the browser?

Yes, and a stack is ordinary work here. Multi-channel LIF and TIFF stacks open with independent brightness and color per channel, a slice stepper to move a plane at a time, and maximum intensity, average, or sum projections. There is no Bio-Formats setup and no admin rights, so a student's managed laptop opens the same stack as the rig workstation.

Does Conspecta do 3D reconstruction or filament tracing?

No. Surface reconstruction and filament tracing are outside what Conspecta does, and if tracing dendrites is your core output you should keep the workstation tool that does it. On those same stacks Conspecta covers plane-by-plane viewing, a 3D view you can rotate, projections, counting per plane, intensity, and colocalization with Pearson's, Manders', and Costes thresholding, every number still tied to the animal and the region.

How do I keep track of which section came from which animal?

Animals, brain regions, tissue sections, and injection sites are registered as samples, and every image and measurement attaches to the tissue it was taken from. The sample's Connections tab lists the images, the analysis, and the figures that came out of it, so a figure panel still points back to the animal after someone reorganizes a folder.

How much does image analysis cost?

Conspecta is free for you and one collaborator, with no credit card. Academic teams pay a flat per-lab rate for a shared workspace rather than a per-seat license, so a rotation student does not add a line to the invoice. Detecting objects with a model runs on our servers and draws on the monthly compute usage a paid plan includes, counted per image. Brightness-cutoff detection, the guided builder, and every bit of tuning before you commit a run happen in your browser and are free.

See it on your own stack

Upload a confocal z-stack and run a count. Every number stays attached to the image and the channel it was measured from.

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