Archive of CMCI developed tools
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
- 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
- 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