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Image analysis guides

How to measure microscope images, electron micrographs, western blots and gels: set the scale, measure length and area, count cells and particles, quantify bands and fluorescence. Each guide gives the steps in ImageJ and Fiji, then the same job in LabCanvas Image Analysis, in your browser.

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LabCanvas Image Analysis measuring nuclear translocation: forty numbered cells with their nuclei and cytoplasm rings outlined, and the assay panel with the cell count and the nuclear/cytoplasmic ratio
20 min read

Image Analysis in LabCanvas: a complete guide to every tool and setting, with examples

Every tool in LabCanvas Image Analysis, tab by tab, with its settings and a real example: image check, display and scale, stacks and Z projection, background subtraction, filters, thresholds and binary operations, ROIs and Set measurements, Analyze Particles, a pixel classifier, spots, cell counter, western blot densitometry, colocalisation, colour deconvolution and eleven guided assays.

LabCanvas Image Analysis counting nuclei: the image with numbered particle outlines, the Count panel on the right and the results table under the image
5 min read

LabCanvas Image Analysis: measure microscopy images, western blots and gels in your browser

How to measure images in LabCanvas Image Analysis: guided assays (nuclear translocation, spots per cell, wound healing, FRAP, calcium, tracking, branching), western blots with a ladder and total-protein normalisation, cell counting with a trainable classifier, ROIs with ImageJ definitions, on the raw pixel values, with results sent to Graphs.

How-to guides

The same synthetic nuclei image counted in two programs: on the left ImageJ 1.54f with 70 nuclei outlined in yellow and a Summary of count 70, average size 40.648 µm²; on the right LabCanvas Image Analysis with 70 numbered nuclei and the line 70 particles, mean 40.47 µm²
22 min read

ImageJ vs LabCanvas Image Analysis: an honest comparison

ImageJ/Fiji or LabCanvas Image Analysis? Six everyday jobs done in both, six newer ones (macros, vendor files, 3D, StarDist, big images) and which to use.

ImageJ 1.54f with its menu bar and toolbar, a synthetic nuclei image with 70 nuclei outlined and numbered by Analyze Particles, and the Summary and Results tables giving the count, area and mean intensity
11 min read

How to use ImageJ: a beginner's tutorial for the 10 everyday jobs (2026)

How to use ImageJ and Fiji: get started, open an image, then 10 everyday jobs (scale, measure, threshold, count, background, blots) with exact menu paths.

ImageJ Set Scale dialog over a synthetic stage micrometer: a line from 0 to 100 divisions measures 1,538.46 pixels, Known distance 1000 µm gives 1.5385 pixels per µm (0.65 µm per pixel), and a 200 µm scale bar sits in the lower right corner as an overlay
10 min read

How to set the scale and add a scale bar in ImageJ (with a calibration image to practise on)

Set the scale in ImageJ (Analyze › Set Scale) from a micrometer, scale bar or pixel size, add a scale bar, and practise on a free calibration image.

ImageJ quantifying a synthetic western blot: eight lanes selected with Analyze › Gels, the Plot Lanes window with a target and a loading-control peak per lane, and a table of band areas and fold changes, lane 8 at 8.736-fold
12 min read

Western blot quantification in ImageJ, step by step (and the 3-click way)

Quantify a western blot in ImageJ with Analyze › Gels, normalise to a loading control or total protein, and get fold change. Plus a 3-click way.

ImageJ 1.54f counting the synthetic nuclei sample: 70 nuclei outlined in yellow and numbered after an Otsu threshold, Fill Holes and Watershed, the Analyze Particles dialog with a size of 7 to Infinity µm² and Summarize ticked, and the Summary table with a count of 70
10 min read

How to count cells in ImageJ (automatic and manual)

Count cells in ImageJ: automatic (threshold, Watershed, Analyze Particles) or manual (Cell Counter, Multi-point), plus cells per mm² and % positive.

ImageJ measuring a synthetic SEM image of nanorods at 2.5 nm per pixel: three rods measured with straight lines (810.9, 585.5 and 850.2 nm in the Length column) and a fourth outlined with the wand (Area 17,050.0 nm²) in the Results table
8 min read

How to measure length and area in ImageJ (with the right units)

Measure length and area in ImageJ: set the scale, draw lines or area selections (polygon, wand, threshold), press Measure, and get µm and µm², not pixels.

ImageJ Analyze Particles on a synthetic SEM image of a perovskite film: 118 whole grains outlined in yellow and numbered, grains cut by the edge left out, the Results table with the area and Feret diameter of each grain, and the Summary row with Count 118 and Average Size 39,344.6 nm²
14 min read

Grain size analysis in ImageJ (SEM, ASTM E112) + grain size number calculator

Measure grain size from SEM images in ImageJ: closed boundaries, Analyze Particles, then ASTM E112 G from mean area or intercept, with a worked example.

ImageJ 1.54f measuring a synthetic leaf with an insect hole beside a ruler: the scale set from 15 cm of the ruler, the leaf thresholded in red, and the Summary and Results tables giving one leaf of 36.111 cm² with Include holes
9 min read

How to measure leaf area with ImageJ (or from a phone photo, in the browser)

Measure leaf area in ImageJ from a photo or scan: set the scale from a ruler, threshold the leaf, run Analyze Particles in cm², with or without holes.

ImageJ 1.x windows as ImageJ.JS shows them in a browser tab, here in ImageJ 1.54f: the menu bar and toolbar, the Threshold window with the Default method and Dark background, a synthetic nuclei image with the nuclei in red, and a Summary table counting 70 nuclei
8 min read

ImageJ online: can you run it in a browser? (ImageJ.JS, and a faster way)

Yes: ImageJ.JS runs ImageJ 1.x in your browser via CheerpJ (WebAssembly). What works, what doesn't, Fiji online, iPad and Android, and a faster option.

ImageJ 1.54f counting the nuclei sample with Analyze Particles: seventy nuclei outlined in yellow and numbered, the Results table, and a Summary row of 70 nuclei with an average size of 40.394 µm²
13 min read

Best ImageJ alternatives in 2026 (free, online and desktop)

The best ImageJ alternatives compared: browser tools, Fiji, CellProfiler, QuPath, ilastik, napari, Icy, MIPAR, and Image Lab and Empiria for blots.

ImageJ 1.54f measuring a synthetic SEM image of MoS₂ flakes: 33 flakes outlined in yellow after Analyze Particles, and the Results table with the area, Feret diameter and MinFeret of each flake
10 min read

Lateral size of 2D flakes (graphene, MoS₂) from SEM or TEM in ImageJ

Measure graphene or MoS₂ flake lateral size in ImageJ: scale, threshold, Analyze Particles with Feret diameter, edge flakes, overlaps and a size histogram.

ImageJ Analyze Particles on a synthetic TEM image of gold nanoparticles: 136 particles outlined in yellow and numbered, the Results table with the area and Feret diameter of each, and the Summary row with Count 136, Average Size 133.855 nm² and mean Feret 13.777 nm
11 min read

Analyze Particles in ImageJ, explained (every option, with examples)

Every Analyze Particles option in ImageJ, shown on a TEM image: size, circularity, Show, Exclude on edges, Include holes, and why it finds 0 or 1 particle.

ImageJ calcium imaging analysis: the ΔF/F₀ macro in the editor, the stacked ΔF/F₀ traces of 20 cells from a synthetic GCaMP movie, and the Peaks table with F₀, peaks and maximum ΔF/F₀ per cell
8 min read

Calcium imaging analysis in ImageJ: ΔF/F₀ traces step by step

Calcium imaging in ImageJ: ROIs on cells, Multi Measure, background, F₀ (first frames or a percentile), ΔF/F₀ = (F − F₀)/F₀, traces and peak counting.

ImageJ 1.54f after counting the synthetic nuclei sample: 70 nuclei outlined in yellow and the Summary window with a count of 70, total area 2845.326 µm² and an average size of 40.648 µm²
9 min read

CellProfiler vs QuPath vs ImageJ: which image analysis software should you use?

CellProfiler, QuPath or ImageJ/Fiji? A fair comparison by job (batch cell measurements, whole slides, general analysis), with a nuclei count step by step.

ImageJ 1.54f on a synthetic two-channel image: the green and magenta composite, the 2D histogram with the Costes thresholds (566 and 480) as cyan lines, and the macro’s result, Pearson’s r 0.529, tM1 0.220 and tM2 0.215
10 min read

Colocalization analysis in ImageJ: Pearson vs Manders and Costes thresholds

Colocalization in ImageJ and Fiji: what Pearson’s r and Manders’ M1/M2 each answer, Costes thresholds, Coloc 2 vs JACoP, a worked example and pitfalls.

ImageJ counting colonies on a synthetic photo of a 60 mm dish: Analyze Particles outlines and numbers 60 colonies, and the Summary table gives a count of 60 and an average size of 1.275 mm²
8 min read

Count bacterial colonies in ImageJ (or from a plate photo, free online)

Count colonies in ImageJ: oval on the dish, threshold, Watershed, Analyze Particles. Then CFU/mL from the count and dilution, with a worked example.

ImageJ measuring the contact angle of a sessile water drop with the Angle tool: lines along the baseline and the tangent at each contact point, and a Results table reading 72.0, 72.0 and 63.6 degrees
11 min read

Measure contact angle from a drop photo in ImageJ

Measure contact angle in ImageJ with the Angle tool along the tangent, or from drop height and base width: θ = 2·arctan(2h/d). Worked example, plugins.

ImageJ 1.54f counting γH2AX foci on a synthetic image: thirty nuclei outlined in yellow with a white cross on every focus, an enlarged nucleus, and the Find Maxima dialog with a prominence of 300
7 min read

Count γH2AX or 53BP1 foci per nucleus in ImageJ (Find Maxima, step by step)

Count γH2AX or 53BP1 foci per nucleus in ImageJ: nuclei as ROIs, Find Maxima with the right prominence, counts per nucleus and % of cells with ≥5 foci.

ImageJ Plot Profile across the lattice fringes of a synthetic HRTEM gold nanocrystal: a 21-pixel-wide line across the {111} fringes and the profile with the dark minima numbered 0 to 10, giving d = 2.36 nm ÷ 10 = 0.236 nm
11 min read

How to measure d-spacing from HRTEM lattice fringes in ImageJ (profile and FFT)

Measure d-spacing in ImageJ: a wide line across 10 fringes and Plot Profile (d = L ÷ N), or FFT spots read with Measure. Worked on Au (111), 0.235 nm.

ImageJ 1.54f Color Threshold on a synthetic H-DAB section: hue 0–30 and saturation 40–255 in HSB select the brown DAB-positive cells, shown in red, 7.42% of the section
9 min read

IHC DAB quantification in ImageJ with colour deconvolution

Quantify DAB IHC in ImageJ/Fiji: colour deconvolution with H-DAB vectors, % positive area, optical density, and why DAB intensity is not linear.

ImageJ measuring nanorods in a synthetic SEM image: Analyze Particles outlines and numbers 36 rods, and the Results table lists each rod’s circularity, Feret (length), MinFeret (width), AR and solidity
9 min read

Feret diameter, circularity, aspect ratio and solidity in ImageJ, explained

What ImageJ shape descriptors mean: Feret and MinFeret, circularity, AR, roundness and solidity, with formulas, drawn shapes and real TEM and SEM numbers.

ImageJ 1.54f on a synthetic image of 140 crowded nuclei: on the left, an Otsu threshold with Watershed outlines only 90 objects, merging touching nuclei, missing dim ones and flooding the bright corner; on the right, the true label image turned into ROIs outlines all 140 nuclei
13 min read

Deep-learning cell segmentation in Fiji: StarDist, Cellpose and Weka (step by step)

When a threshold fails, segment cells in Fiji with StarDist, Cellpose or Trainable Weka: install, settings, then label image to ROIs and measurements.

ImageJ 1.54f showing two neighbouring synthetic SEM tiles side by side: the right edge of tile 1 and the left edge of tile 2 are boxed in red, because they show the same 78-pixel strip of the sample
8 min read

Stitch microscope tiles in Fiji (Grid/Collection stitching, step by step)

Stitch overlapping microscope tiles in Fiji with Grid/Collection stitching: grid type, overlap, file names, fusion, and why an ImageJ montage is wrong.

ImageJ 1.54f, the plain ImageJ 1.x download: its eight menus and toolbar, and Help › About ImageJ showing the version, the Java it runs on and the public-domain notice
7 min read

Fiji vs ImageJ: what's the difference, and which should you download?

Fiji is ImageJ with plugins, Bio-Formats, an updater and scripting built in; ImageJ2 is the rewrite underneath. A comparison table and which to download.

ImageJ FRAP analysis of a synthetic cell: frames before the bleach, just after it and recovered, with the bleach, cell and background ROIs, and the Curve Fitting result of an exponential recovery (mobile fraction 0.80, half-time 2.78 s)
8 min read

FRAP analysis in ImageJ: mobile fraction and half-time, step by step

FRAP in ImageJ: bleach, reference and background ROIs, Multi Measure, double normalisation, an exponential recovery fit, then the mobile fraction and t½.

ImageJ 1.54f quantifying the synthetic western blot with Analyze › Gels: eight lane rectangles numbered on the blot (lane 1 with Select First Lane, lanes 2 to 8 with Select Next Lane) and the Gel Analyzer Options dialog with Invert peaks on for dark bands
9 min read

Free western blot quantification software (now that Image Studio Lite is gone)

Image Studio Lite is discontinued. Quantify western blots free in ImageJ (Analyze › Gels), step by step, with Image Lab and IOCBIO Gel compared.

ImageJ’s Help › About ImageJ window showing version 1.54f, with the version, the Java version and the macro getVersion() result outlined
6 min read

How to cite ImageJ and Fiji (with a methods sentence to copy)

Cite ImageJ (Schneider et al. 2012), Fiji (Schindelin et al. 2012) or ImageJ2 (Rueden et al. 2017): DOIs, APA, Vancouver, BibTeX and methods sentences.

ImageJ 3D Projection dialog set to Brightest Point, Y-Axis, 0.50 micron slice spacing, 360 degrees in 10 degree steps with Interpolate ticked, beside four frames of the rotating projection of a synthetic bead Z-stack at 0, 30, 60 and 90 degrees
8 min read

3D projection and 3D viewing in ImageJ (Image › Stacks › 3D Project)

Make a rotating 3D view of a Z-stack with Image › Stacks › 3D Project in ImageJ, set the slice spacing, use Orthogonal Views, or Fiji's 3D Viewer.

ImageJ 1.54f rotating the synthetic nuclei sample by 15 degrees with Enlarge image and Preview ticked, above a Results table that compares the area, mean, minimum, maximum and pixel width after crop, rotate, resize, scale and 8-bit conversion
8 min read

Crop, rotate, resize and convert images in ImageJ (without changing your data by accident)

How to crop, rotate, resize, zoom and convert to 8-bit or grayscale in ImageJ, and what each command does to pixel values and the scale, measured.

ImageJ 1.54f montage of a synthetic test image: the known sample, the same blurred with a Gaussian PSF plus noise, the noise-only result of FD Math Deconvolve, and the sharp result of 30 Richardson–Lucy iterations, above an ImageJ plot in which two beads 6 pixels apart are resolved only after Richardson–Lucy
9 min read

Deconvolution in ImageJ and Fiji: what it does and how to run it

What deconvolution does (the PSF, Richardson–Lucy), why FD Math Deconvolve fails on real images, and how to run Richardson–Lucy in ImageJ and Fiji.

ImageJ 1.54f on a synthetic nuclei image with horizontal stripes: the striped image, its FFT power spectrum, the bandpass filter, the filtered image with the stripes removed, Find Edges, and the edges thresholded and filled (68 objects)
9 min read

FFT bandpass filter and edge detection in ImageJ (with before/after examples)

FFT in ImageJ step by step: Process › FFT, Bandpass Filter settings, stripe removal and Find Edges, with before/after pictures and when filtering is safe.

ImageJ 1.54f on a deliberately saturated copy of the synthetic nuclei image: in the HiLo lookup table with the display at 0 to 65535 the clipped nuclei are red, and the Analyze › Histogram window reads Max 65535 and Mode 65535
9 min read

Check for saturated pixels in ImageJ: histogram, HiLo LUT and the numbers

Check saturation in ImageJ with Analyze › Histogram, the HiLo LUT and Min/Max, on a clipped example with its spike at 65535 and what it does to data.

ImageJ showing the synthetic nuclei sample in the Fire lookup table with a calibration bar from 316 to 5200, next to the Calibration Bar dialog with its location, colours, number of labels, decimal places, font size and Overlay options
8 min read

LUTs in ImageJ: which lookup table to use (and colour-blind-safe choices)

ImageJ lookup tables compared on one image: Grays, Fire, viridis, HiLo and the rest, how to add a calibration bar, and colour-blind-safe channel colours.

ImageJ 1.54f main window with Edit › Options › Memory & Threads open: Maximum memory in MB and Parallel threads outlined, and the status bar showing the ImageJ and Java versions
9 min read

ImageJ and Fiji on a Mac: install, Apple Silicon and "can't be opened" fixes

Download ImageJ or Fiji for Mac (Apple Silicon or Intel), fix "can't be opened" and "damaged" errors, set the memory, and the no-install option.

ImageJ 1.54f running a recorded macro: the macro editor with eight recorded lines, the Summary table with 70 nuclei and an average size of 40.394 µm², and the numbered outlines of the nuclei
8 min read

ImageJ macros for beginners: record a macro and batch-process a folder

Record an ImageJ macro with Plugins › Macros › Record, run it from the editor, then batch-process a folder with Process › Batch › Macro. Step by step.

ImageJ 1.54f preparing a time-lapse movie: a synthetic filament time-lapse at frame 21 with a 10.0 s time stamp and a 10 µm scale bar, and the Scale Bar dialog with Overlay and Label all slices marked
7 min read

Make a movie from an image stack or time-lapse in ImageJ (AVI, GIF, MP4)

Turn a folder of frames or a time-lapse stack into an AVI, GIF or MP4 in ImageJ: Image Sequence, a time stamp, a scale bar, frame rate, and saving.

ImageJ Plot Profile of a straight line across the nuclei sample: one peak per nucleus, two touching nuclei as a double peak, the List, Data, More and Live buttons, and the Data menu opened
8 min read

Plot Profile in ImageJ: line scans, wide lines and intensity profiles

Plot Profile in ImageJ: draw a line, press Ctrl K, set the line width to average noise, copy the values, plot two channels and profile a rectangle.

ImageJ 1.54f on the synthetic two-channel NF-κB sample: 40 nuclei found by Analyze Particles with Add to Manager, outlined and numbered on the image with Show All and Labels, and the ROI Manager listing them beside it
8 min read

ROI Manager in ImageJ: measure many regions, save them and open them anywhere

Open the ROI Manager in ImageJ (Analyze › Tools › ROI Manager), add ROIs with T, measure them on every channel, save RoiSet.zip and reopen it later.

ImageJ 1.54f threshold methods compared on a synthetic nuclei image: one tile per entry of the Threshold list, from Default and Huang to Triangle and Yen, thresholded pixels in red with each threshold value and %Area
12 min read

ImageJ threshold methods compared, with pictures

All 16 ImageJ auto threshold methods on one image, with the threshold and % area each gives, which method suits which image, and how to apply it.

ImageJ 1.54f Memory and Threads dialog (Edit › Options › Memory & Threads) with the maximum memory in MB, under the ImageJ main window whose status bar shows ImageJ 1.54f on 64-bit Java 21
7 min read

Install ImageJ or Fiji on Windows 10 and 11

Download and install Fiji or ImageJ on Windows 10 and 11: the right zip, where to unzip it (not Program Files), Java, memory, and where files go.

ImageJ kymograph of the synthetic transport sample made with Reslice, its five particle streaks measured with straight lines, and a Results table of velocities from −1.394 to 1.039 µm/s
9 min read

How to make a kymograph in ImageJ and measure velocities

Make a kymograph in ImageJ: a line along the track, Image › Stacks › Reslice, then a line on each streak gives velocity = Δx ÷ Δt, with a worked example.

ImageJ Z Project dialog over a synthetic bead Z-stack, slice 8 of 15 on screen: Start slice 1, Stop slice 15, and the Projection type list open with Max Intensity and Sum Slices marked
8 min read

Z Project in ImageJ: maximum, average and sum projections compared

Image › Stacks › Z Project in ImageJ: what Max Intensity, Average, Sum Slices, SD, Min and Median give, when Sum beats Max, and how to check depth.

ImageJ 1.54f measuring fluorescence on a synthetic 16-bit nuclei image: one cell outlined and three background squares from the ROI Manager, and the Results table with Area, Mean, IntDen and RawIntDen for each
9 min read

How to measure fluorescence intensity in ImageJ (Mean, IntDen, RawIntDen and CTCF)

Measure fluorescence in ImageJ: Mean, IntDen and RawIntDen explained, CTCF = IntDen − Area × background worked through, and the 8-bit and saturation traps.

ImageJ showing the two-channel sample as a green and magenta composite, with the Channels Tool set to Composite and its More menu open at Split Channels, Merge Channels and the channel colours
9 min read

Merge, split and overlay channels in ImageJ (and make a composite figure)

Merge channels in ImageJ with Image › Color › Merge Channels, split them with Split Channels, overlay with Add Image, and build a colour-blind-safe figure.

ImageJ histograms of a synthetic western blot: on the left the contrast was pushed too far and applied, with 21% of pixels at 255 and 3.9% at 0; on the right a linear range of 15000 to 57000 converted to 8-bit, with nothing clipped
10 min read

Image integrity: what you may and may not do to microscopy and blot images

What journals allow when you adjust microscopy and blot images: linear whole-image changes, gamma disclosed, no cloning or selective edits, in ImageJ.

ImageJ 1.54f on the synthetic TEM image of gold nanoparticles: 136 particles outlined in yellow after Otsu, Fill Holes, Watershed and Analyze Particles, the Distribution histogram of Feret diameters (n 136, mean 13.777 nm, SD 1.585 nm) and the Results table with one row per particle
10 min read

Nanoparticle size distribution from TEM images in ImageJ (step by step)

Nanoparticle size from TEM in ImageJ: scale, threshold, watershed, Analyze Particles with Feret, then the size histogram and mean ± SD, worked through.

ImageJ 1.54f measuring nanorods on a synthetic SEM image: 36 rods outlined in cyan and numbered, rods cut by the frame outlined in orange and left out
7 min read

Nanorod and nanowire length, width and aspect ratio from SEM images in ImageJ

Measure nanorod and nanowire length, width and aspect ratio from SEM images in ImageJ: Feret, MinFeret, fit ellipse, edge rods, and why not to watershed.

ImageJ skeleton of two synthetic branched cells after Process › Binary › Skeletonize, beside the length macro table: 1,719 skeleton pixels, 24 end points, 68 junction pixels, 343.8 µm by pixel count and 401.5 µm with steps of 1 and 1.414, against 383.2 µm drawn
9 min read

Neurite length and branching in ImageJ: Skeletonize and Analyze Skeleton

Neurite length and branching in ImageJ: threshold, Process › Binary › Skeletonize, then Analyze Skeleton (Fiji) or a macro. Why diagonal steps matter.

ImageJ 1.54f measuring the nuclear/cytoplasmic ratio on a synthetic p65 image: forty cells with the nucleus outlined in cyan and a cytoplasm ring in yellow, numbered, beside a Results table of nucleus mean, ring mean and N/C for each cell
8 min read

Nuclear/cytoplasmic ratio in ImageJ: quantify NF-κB, YAP or TFEB translocation

Measure the nuclear/cytoplasmic ratio in ImageJ step by step: nuclei from DAPI, a cytoplasm ring with Enlarge and Make Band, and an N/C table per cell.

ImageJ 1.54f Image › Properties on a synthetic 16-bit nuclei image saved as TIFF: pixel width and height 0.325 micron read from the file, and the title bar giving 166.40 × 166.40 microns
9 min read

How to open .czi, .nd2, .lif and other microscope files in ImageJ (Bio-Formats)

Open Zeiss .czi, Nikon .nd2 and Leica .lif files in ImageJ with Bio-Formats (built into Fiji), keep the pixel size, and fix "Unsupported format".

ImageJ 1.54f with a synthetic CT phantom opened from a DICOM series as a 12-slice stack: two oval ROIs and the Results table, 40.2 HU in soft tissue and -799.6 HU in an air-filled region
7 min read

Open DICOM files in ImageJ (and a series as a stack)

Open DICOM files in ImageJ with File › Open, a whole series as a stack with Import › Image Sequence, read the tags, measure HU, and open compressed DICOM.

ImageJ Z Project dialog set to Max Intensity over frames 1 to 50 of a synthetic particle time-lapse, and the maximum projection showing the path of every particle as a trail
11 min read

Particle tracking in ImageJ (TrackMate) and MSD: a practical guide

Track particles in ImageJ with TrackMate (Fiji) or Find Maxima, then get the diffusion coefficient from the MSD: MSD = 4Dt in 2D, with a worked example.

ImageJ measuring a sample SEM image of anodic alumina: 160 pores outlined in yellow, the Analyze Particles dialog, a Results row with %Area 34.666 (the porosity, Otsu cut at 100) and a Summary of 160 pores with an average size of 3,098.564 nm²
9 min read

Porosity and pore size from SEM images in ImageJ (AAO, membranes, coatings)

Porosity and pore size from an SEM image in ImageJ: threshold the pores, read %Area as porosity, then Analyze Particles for pore areas and diameters.

ImageJ 1.54f with the synthetic nuclei sample, the count-nuclei.ijm macro open in the macro editor, and the Results table after running it: 70 rows and a mean area of 40.394 µm²
7 min read

Use ImageJ from Python with PyImageJ (a gentle start)

Install PyImageJ, start ImageJ from Python with imagej.init, run your ImageJ macro, and get the image as NumPy and the Results table as pandas.

ImageJ 1.54f Subtract Background on the synthetic nuclei sample: the original with its uneven background, rolling-ball radius 5, 15, 50 and 150 pixels, and the background that radius 50 found; radius 5 leaves only cross-shaped remains of the nuclei, radius 50 gives a flat floor with the nuclei intact
9 min read

Rolling-ball background subtraction in ImageJ: how to choose the radius

Subtract background in ImageJ: Process › Subtract Background, a rolling ball radius at least the largest object's, Light background off for fluorescence.

ImageJ wound healing analysis of a synthetic scratch time-lapse: four frames at 0, 6, 14 and 22 hours with the open area outlined in yellow, closing from 118,259 µm² to 30,031 µm² (74.6% closed)
9 min read

Wound healing (scratch) assay analysis in ImageJ: % closure step by step

Measure a scratch wound in ImageJ: variance filter, threshold and Analyze Particles per frame, then % closure and closure rate, with a worked example.

ImageJ Sholl analysis of a synthetic neuron with a macro: cyan circles every 5 µm around the cell body, red dots at each crossing, the Sholl plot peaking at 18 crossings at 30 µm, and the table of crossings per radius
9 min read

Sholl analysis in ImageJ/Fiji and online (step by step)

Sholl analysis step by step: circles around the cell body, crossings per radius, the Sholl plot, critical radius and ramification index, in Fiji (SNT) or with an ImageJ macro.

ImageJ 1.54f result on a synthetic endothelial tube network: the skeleton drawn in yellow over the phase-contrast image, 125 junctions as red circles and 46 closed meshes shaded blue
8 min read

Tube formation assay quantification in ImageJ (and the Angiogenesis Analyzer)

Quantify a tube formation assay in ImageJ step by step: total tube length, junctions, segments and meshes, plus the Angiogenesis Analyzer and AngioTool.

ImageJ 1.54f masks of synthetic TEM gold nanoparticles without and with Process › Binary › Watershed, each particle in its own colour: touching particles merged into 74 objects before, split into 136 after
8 min read

Watershed in ImageJ: separate touching particles (and when not to)

Split touching nuclei and nanoparticles with Process › Binary › Watershed in ImageJ, with before and after counts, and why it cuts nanorods to pieces.