Augmented Microscopy

Augmented Microscopy integrates and automates all typical microscopy steps from image capture to publication-ready data.

Quickly, and simply:

  • Cells are automatically imaged (end-point, tiling, Z-stacks, time-lapse). 
  • Image processing enhances images for downstream analysis.
  • Cellular components are identified and analyzed automatically.
  • Qualitative and quantitative information is extracted and displayed.
  • Annotation of single or sequential images is available on-screen, in real time.
  • Video clips can be generated with a single click.

Augmented Microscopy creates a 'map' with key analytical information, helping you to make informed decisions faster.



With Gen5 software, images can be captured by a “manual” mode for lower throughput, typically imaging a few samples at a time. “Experiment” mode automates image capture and analysis in multiple wells and can include both imaging and plate reading, plus other steps required for some live cell applications, like reagent injection, shaking and incubation.  In both modes, the intuitive interface and automated functions like “find image”, Auto Exposure, Auto LED intensity, Autofocus (including image-based and laser autofocus) capturing images simple and efficient.  Live cell kinetic sequences can also be completely automated, from initial image capture through movie creation. Images captured in Gen5 are ready for automated processing an in-depth quantitative analysis.

Manual mode screen
Experiment screen

Gen5’s manual mode interface (left) and experiment mode (right) 96-well image display.


Image preprocessing, including background flattening and image smoothing, optimize images for downstream analysis. Image processing features in Gen5 include:

  • Image stitching, which allows multiple tiled images (montages) to be software aligned, creating a complete picture of the entire sample with great accuracy, to provide more meaningful data.
  • Z-projection, which is essential for 3D imaging applications like spheroid, tumoroid and hanging droplet assays whose biology can’t be captured adequately with an objective’s typical depth of field.
  • Digital phase contrast overcomes the meniscus effect often seen in 96- and 384-well plates during brightfield imaging. Digital phase contrast is an enhancement technique that minimizes uneven illumination and creates a more consistent contrast across the image for better visualization.

Stitched image of 18 row by 12 column montage
Stitched image of 18 row by 12 column montage shows entire well of a 6-well plate, with hanging drop insert and spheroid. See Application Note for details.
HCT 116 tumoroids, single plane images (A), (B), (C) are z-stacked and z-projected (D) in Gen5
HCT 116 tumoroids, single plane images (A), (B), (C)
are z-stacked and z-projected (D) in Gen5. Learn more in the Application Note.


Gen5 offers powerful image analysis for a broad range of live and fixed cell imaging. Automated cell counting, label-free cell counting, transfection efficiency and nuclear translocation analyses are facilitated with features like dual masks for nuclear and cytoplasmic measurements, dynamic thresholding and custom object-level metrics.

Nuclear and cytoplasmic masks in Gen5

Nuclear and cytoplasmic masks in Gen5


After image analysis, it’s common to annotate specific details in the image for publication or other documentation purposes. Gen5 has a built-in annotation tool, so there’s no need to export image files to another software package. Live cell kinetics can be captured and a .wmv or .mp4 file generated automatically right within Gen5. Still images can be exported in a variety of common formats.  These features make publication-ready images and data from Gen5 available with a few clicks.

Hella video
Gen5 automatically generates video of time lapse images, like this from a label-free wound healing assay.
Confluency graph
Quantitative analysis in Gen5

Annotate images directly in Gen5


See what other BioTek imaging users are doing! Search BioTek’s technical resources for citations, application notes, webinars and more, and peruse our Customer Spotlights for all the latest research using Augmented Microscopy.

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