CMCI works

Archive of CMCI developed tools

May 27, 2016

This site is a catalogue of bioimage analysis software tools developed by Kota Miura. Tools have individual pages and are categorized as follows:

Analysis: starting with either image or text file data, these tools outputs numerical results of analysis.
Processing: tools that process images for further detailed analysis.
Tools: small utilities for image analysis
Visualization: tools for data visualization.
General Instructions: instructions common to various tools, such as installation protocol.

For questions and bug reports, please post them as a new issue in the github repository of each tool.

Pages in Categories

Analysis
- centrosome centrosome distance : Measures centrosome-centrosome distances in multiple nucleus
- VecField 2D : Gradient-based optical flow estimation
- KMeans Points Clustering : Labeling non-connected components as a sinlge object using K-means clustering.
- Nucleus Rim Measurement : Measurement of intensity changes at the periphery of nucleus over time
- ClusterIndex : Quantification of the degree of cell clustering by computing 'Cell Cluster Index'
- DotLinker : Global optimization of particle linking.
- Spindle Frap-Flip Analyzer : Analyze protein dynamics within spindle
- FrapCalc : Analyzes FRAP curves with various models
- 3D Intensity Profile : Measurement of intensity profile in 3D space
- Primodium Analysis : An analysis workflow for quantifying cellular dynamics during lateral line formation of Zebrafish
- Batch PIV : Batch processing for Particle Image Velocitometry (PIV) plugin to measure 2D time series
General_instructions
- Installation of Apache Commons Math : How to add Apache Commons Math library to ImageJ
- Installing Scripts to ImageJ : Various methods to run script in ImageJ / Fiji
Processing
- Affine Transform 3D : Affine transformation of 3D image data based on pairs of feature points
- Easy 3D Stack Concatenater : Concatenate 3D stacks with registration using user-provided landmark points
- Easy 3D Stack Concatenater point ROIs : Concatenate 3D stacks with manually selected point ROIs
- BleachCorrector : Three different intensity correction methods for the intensity loss by photobleaching of sample
- headless scripts : A collection of scripts for simple computing in cluster
- Cell Boundary Detection By PeakFitting : Cell boundary detection and segmentation based on peak fitting
Tools
- Text to Stack3D : Generates a 3D volume stack with defined spots in a text file
- NaN to 0 : Convert NaN pixel values to 0 in 32bit images
- List XY Resolutions : prints out XY scale of all images in a folder
- DropScript : Assists ImageJ scripting using external editor.
Visualization
- XYZ projection : Generates single image with XY, XZ, YZ projections
- 3DTrackViewer : Visualization of 3D tracking results in ImageJ 3Dviewer.
- SeeSaw 3Dprojector : Animated 3D projection for viewing it as if it is 3D.