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Bioimage Analytics

Quantitative analysis
of microscopy images.

Cell-by-cell measurements, fibre structure and 3D organization from your microscopy images.

See the examples Request a quote

Widefield & confocal 2D & 3D

A supplied 3D rendering of segmented cells, with individual objects shown in different colours.
3D cell segmentation Individual cells identified within a 3D microscopy stack.

Microscopy

Examples

From image to result

Analysis for your
research question.

Review the masks against the raw images and check the measurements. Receive figures, tables and methods text for your study.

Our analysis workflow

Built in-house.Our team uses its own software for your analysis project.

Pilot requests are open

Start with
a few images.

Tell us what you imaged and the question behind it. Each pilot is quoted after we review a few sample images.

  1. 01
    Share your question

    Describe your images and desired readout.

  2. 02
    Agree on the pilot

    We review sample images and prepare a quote.

  3. 03
    Review the pilot

    Check the masks and first measurements.

Describe your images and the measurements you need. We arrange sample sharing after you send the form.

analysis@tissueforgebio.com

Bioimage Analytics / Cell-by-cell measurements

Cell-by-cell measurements

Measure marker distribution in individual cells, with their location and neighbours.

Raw fluorescence microscopy image of a crowded cell culture.
Raw imageThe original microscopy field.
The same microscopy field with nuclei coloured by each cell's nucleus-to-cytoplasm marker ratio.
Marker distributionSame field. Blue: lower nucleus-to-cytoplasm ratio; orange: higher.
40,910Cells passed quality checks.
1.4×Mean sparse-to-crowded marker ratio across 26 wells.
Maps of local cell density and nucleus-to-cytoplasm marker ratio across the same well.
Location within the wellLocal cell density and marker distribution, mapped together.
Well-average marker intensity across seeding densities for two reagents.
Well-average intensityOne mean intensity for each well.
Cell-by-cell nucleus-to-cytoplasm marker ratios across local cell density for two reagents.
Cell-by-cell marker ratios40,736 cells plotted. Vector chart ↗

The 1.4× result compares nucleus-to-cytoplasm marker ratios in sparse (<100 cells/mm²) and crowded (>400 cells/mm²) regions of each well, then averages those comparisons across 26 wells.

The cell plot retains densities below 1,100 cells/mm² and bins with at least 40 cells. Lines: binned medians; bands: middle 50%.

What you receive Cell masks, per-cell measurements, spatial maps and well summaries.

© TissueForge Biosciences. Not for reuse.
Bioimage Analytics / Fibre structure

Microscopy & measurements

Fibre structure

Compare the microscopy images with maps of fibre direction and alignment. Select any image to enlarge it.

Five example fields, with the original cell-body stain in the top row and fibre-direction maps in the bottom row.
Microscopy and fibre-direction mapsTop: cell-body stain. Bottom: colour shows direction; brightness reflects local alignment.
Fibre-direction map of the Substrate 2 example at 60×.
Fibre direction · 60×Colour shows the direction of the visible fibres.
Fibre-direction colour scale from 0 to 180 degrees.0°180°
Local alignment in the same Substrate 2 field at 60×, including areas of lower directional consistency.
Local alignment · same fieldLower alignment marks areas with less consistent fibre direction.
Local-alignment colour scale from lower to higher directional consistency.LowerHigher
0.92 / 0.61Alignment in Substrate 1 / Substrate 2 at 20×.
18%Disrupted alignment in the cell-covered area of the Substrate 2, 60× field.
1.5 µmMedian apparent fibre width in each 60× substrate example.
Fibre-direction map of a dense layer at 20×.
Dense layer · 20×Alignment: 0.85.
Fibre-direction map of the Substrate 1 example at 60×.
Substrate 1 · 60×Alignment: 0.84.
Lines tracing fibre orientation across a 60× microscopy field.
Fibre-orientation linesLines follow fibre direction; they do not measure fluid flow.
Two plots showing alignment and the share of disrupted alignment across nine example fields.
Alignment across nine fieldsAlignment and disrupted-alignment area for each field. View vector alignment chart
Eight image-derived readouts compared across five example conditions.
Eight image-derived readoutsShape, fibre structure and marker distribution viewed together.

One field per condition. These examples illustrate the measurements; they do not establish treatment effects.

What you receive Direction and alignment maps, per-cell measurements, field summaries and figures.

© TissueForge Biosciences. Not for reuse.
Bioimage Analytics / 3D cell segmentation

3D cell segmentation

Compare 2D and 3D segmentation

The same microscopy stack in all three columns. Select an image to enlarge it.

Raw microscopy

Raw microscopy, viewed from above.Raw microscopy, side view through the same stack.
Top view + side viewOriginal image signal through the culture.

2D segmentation

2D segmentation, viewed from above.2D segmentation, side view through the same stack.
Top view + side viewOutlines from the flattened image do not separate depth.

3D segmentation

3D segmentation, viewed from above.3D segmentation, side view through the same stack.
Top view + side viewCell objects retain their depth and shape.
476 → 637Cells counted in 2D → 3D, example field 1.
+34%More cells counted in this field; not an accuracy measure.
521 → 728Cells counted in 2D → 3D, example field 2.

3D objects and cell counts

Cells segmented as individual three-dimensional objects.
Segmented cellsIndividual cell objects in the culture.
Nuclei segmented as individual three-dimensional objects.
Segmented nucleiIndividual nuclear objects in the culture.
Paired cell counts in two example fields, compared using 2D and 3D segmentation.
Counts in two example fieldsA comparison of segmentation counts.View vector chart

What you receive: cell and nuclear masks, cell counts, and measurements of volume, shape and position.

© TissueForge Biosciences. Not for reuse.
Bioimage Analytics / Structure through depth

Confocal microscopy

Structure through depth

View the same stack in 3D and compare its fibre and nuclear signals by depth.

3D view of a thick culture, with nuclei in blue and cell-body signal in white.
3D view of the stackNuclei in blue; cell-body signal in white.Enlarge 3D image

Fibres coloured by depth, showing a deeper layer crossing beneath upper fibres.
Fibres coloured by depthBlue: upper signal. Orange: deeper signal.
Nuclear signal in the same stack, coloured by depth.
Nuclear signal by depthThe same stack and depth-colour scale.
2 directionsA second fibre-direction population appears around 17–21 µm below the top.
0.93 → 0.1Alignment decreases overall across the displayed 0–29 µm range.
12 µmImage-derived cell-layer thickness in this example.
Three plots from the same stack: fibre-direction distribution, alignment and cell-body and nuclear signal through depth.
Direction, alignment and signalThree profiles from the same confocal stack.
Measured alignment at each depth, decreasing overall from about 0.93 at the top to about 0.1 at 29 micrometres.
Alignment through depthThe measured value at each displayed depth.

These views measure image signal and layer structure. They come from a different culture from the 3D cell-count example.

What you receive Depth-coloured images, 3D views, direction and alignment profiles, and image-derived layer measurements.

© TissueForge Biosciences. Not for reuse.
Bioimage Analytics / Reagent comparison

Reagent comparison

Compare two reagents for the same marker, using cell-level measurements from the same plate.

Raw microscopy image of one example field from the reagent-comparison plate.
Raw imageOne example field from this plate.
The same example field with nuclei coloured by nucleus-to-cytoplasm marker ratio.
Marker distributionThe same field, coloured by nucleus-to-cytoplasm marker ratio.
13 wellsMeasured for each reagent.
1.40Reagent 1: mean sparse-to-crowded ratio.
1.46Reagent 2: mean sparse-to-crowded ratio.
Sparse-to-crowded marker-ratio comparisons for Reagent 1 and Reagent 2, with one point for each of 13 wells per reagent.
Comparison across wellsOne point per well shows the signal difference and its variation.
Nucleus-to-cytoplasm marker ratios across neighbourhood cell density, plotted separately for two reagents.
Cell-by-cell distributionsMarker ratios across local cell density. Vector chart ↗

Each comparison uses nucleus-to-cytoplasm marker ratios in sparse (<100 cells/mm²) and crowded (>400 cells/mm²) regions of the same well. Results shown are from this example plate.

The cell plot shows 40,736 cells after density-range and bin-size filtering. Lines: binned medians; bands: middle 50%.

What you receive Reagent comparisons, well-to-well variation and per-cell measurement tables.

© TissueForge Biosciences. Not for reuse.

Image detail

Original