CELL VOLUME CALC

v2.0

Jython workflow for FIJI/ImageJ — dual-channel fluorescence voxel counting with batch processing, multi-threshold sensitivity sweeping, ROI segmentation, and volumetric CSV output. Modification of the Voxel Counter plugin pipeline. Includes the original ImageJ Macro Language (.ijm) predecessor.

← BACK TO ASTRELT.NET
▷ VOLUMETRIC ANALYSIS

VOXEL CHAMBER

MODE3D COUNT
CHANNELSC0·C1·C2
SAMPLING16-BIT Z
FILES3
✦ DOWNLOAD
CELLVOLUME_JYTHON_V2.PY RECOMMENDED
Optimised batch processor. Histogram-based voxel counting (~50–100× faster than v1.0). Per-sample try/except so one bad image doesn't crash overnight runs. Resume mode, pre-flight summary, progress counters, final batch report. No plugin call at runtime — voxel counting reimplemented natively. Same scientific output as v1.0, faster and more robust.
📥 DOWNLOAD v2.0
CELLVOLUME_MACRO.IJM IJM · LEGACY
Original ImageJ Macro Language implementation. Requires the Voxel Counter plugin (bundled with FIJI). Interactive workflow: opens channel stacks, merges, sweeps 11 thresholds, shows Z-projection tiles for visual selection, flags multi-cell images for manual ROI. Predecessor to the Jython series.
📥 DOWNLOAD IJM
CELLVOLUME_JYTHON.PY LEGACY
Original Jython implementation. Per-pixel Python loops for voxel counting. Functional but slow on large stacks. Included for reference and reproducibility with earlier datasets.
📥 DOWNLOAD v1.0
✦ REQUIREMENTS & CITATION
REQUIREMENTNOTES
FIJI / ImageJ Required runtime. Download at fiji.sc. Jython scripts use Python 2.7 dialect bundled with FIJI. IJM macro uses the built-in ImageJ Macro Language interpreter.
Bio-Formats Bundled with FIJI. Used for virtual stack loading of large .tif/.tiff z-stacks (Jython scripts).
Voxel Counter plugin Bundled with FIJI (Plugins → Analyze → Voxel Counter). IJM macro requires this plugin at runtime. Jython v2.0 reimplements counting natively — no plugin call needed. v1.0 uses the plugin directly. Citation required — see below.
Input format Paired channel files named SAMPLENAME_C0.tif, _C1.tif, _C2.tif (2- or 3-channel). 16-bit z-stacks.
CITATION — Original Voxel Counter Plugin:
This script is a modification of the Voxel Counter plugin for FIJI/ImageJ. The Voxel Counter plugin is distributed as part of Fiji (Schindelin J. et al., Fiji: an open-source platform for biological-image analysis, Nature Methods 9, 676–682, 2012 — doi:10.1038/nmeth.2019). If you use this script in published work, please cite the above and acknowledge the Voxel Counter plugin (available under Plugins → Analyze → Voxel Counter in FIJI) as the basis for the volumetric measurement methodology.
✦ WORKFLOW OVERVIEW
  1. Opens paired channel files (_C0, _C1, _C2) as virtual stacks via Bio-Formats
  2. Sums channels into a 32-bit greyscale stack to amplify signal over noise
  3. Despeckles, applies auto brightness/contrast, saves pre-threshold TIFF
  4. Calculates Default auto-threshold from the middle slice
  5. Applies threshold at 11 sensitivity multipliers (70% → 120% in 5% steps)
  6. Runs binary Open on each threshold to clean cell edges
  7. Displays Z-projection side-by-side for user validation
  8. User selects preferred threshold, cell count, and whether cleanup is needed
  9. For multi-cell or cleanup cases: prompts freehand ROI drawing on chosen threshold
  10. Writes per-sample CSV (all 11 thresholds) and appends to batch summary CSV
✦ CHANGELOG
VERSIONCHANGES
v2.0 CURRENT
  • ⚡ Histogram-based voxel counting (~50–100× faster via ImageProcessor.getHistogram())
  • ⚡ ROI cleanup uses Java-native fillOutside() instead of per-pixel Python loop
  • 🛡 Per-sample try/except — bad images logged and skipped, batch continues
  • ▶ Resume mode — skip already-processed samples on re-run
  • 📋 Pre-flight summary dialog with missing-channel warnings
  • 📊 Final batch summary with per-category counts and error log
  • 🔧 CSV building extracted to reusable helpers; file handles wrapped in try/finally
v1.0 Jython port of the IJM macro workflow. Per-pixel Python loops, single-pass batch, no resume capability, no per-sample error handling. Output values identical to v2.0.
IJM Original ImageJ Macro Language implementation, predating the Jython series. Calls the Voxel Counter plugin directly at runtime. Interactive threshold selection with tiled Z-projection previews and multi-cell flagging dialog. Included for plugin-based workflows and reproducibility with earlier datasets.
jython imagej macro fiji / imagej fluorescence microscopy voxel counting cell biology batch processing z-stack no install
⚙ DEV PANEL
idle
← ASTRELT.EXE