 calculateStateEnergy | calculateStateEnergy : calculates the state energy for modifying segments |
| cellprops3 | cellprops3 : Calculates the shape properties of the region or 'cell'. |
| cellprops5 | cellprops5 : Calculates the shape properties of a region or 'cell'. |
| compConn | compConn : calculates the connectivity of each pixel |
| defineGoodSegs | defineGoodSegs sets the segments to good, bad and 3n set by the watershed algorithm |
| doSeg | doSeg : Segments and saves data in the seg.mat files in the seg/ directory. |
| getRegNames3 | getRegNames3 : contains the names of the parameters used for scoring regions. |
| getSegInfoNames | getSegInfoNames : names for the 19 parameters used to calculate the |
| houseNeuralSimulation | houseNeuralSimulation : calculates output for neural network. |
| intRemoveFalseMicroCol | intRemoveFalseMicroCol : used to remove regions that are not cells. |
| magicContrast | magicContrast : applies a filter to enhance inter-cellular contrast. |
| makeBgMask | makeBgMask : makes a background mask for the phase image |
| makeRegSize | makeRegSize : computes the projections lengths after rotating. |
| makeRegionAxisFast | makeRegionAxis : calculates the principal axis of the segment mask. |
| makeRegionSize | makeRegionSize : computes the projections lengths on the principal axis. |
| perRegionOpti | perRegionOpti : Segmentaion optimization using region characteristics. |
| regionOpti | regionOpti : Segmentaion optimization using region characteristics. |
| removeDebris | removeDebris : removes false positives from microcolony mask |
| scoreNeuralNet | scoreNeuralNet : calculates the scores of regions/ segments using a trained neural network |
| segInfoCurv | segsInfoCurv : Calculates the properties of the segments used for segment scoring. |
| segInfoL2 | segInfoL2 : Calculates the properties of the segments used for segment scoring. |
| segsTLEdit | segsTLEdit : used to visually modify segments in a frame. |
| simAnnealMap | simAnneal: Finds the minimum energy configuration using simulated anneal. |
| ssoSegFun | ssoSegFun : starts segmentation of phase image and sets error flags |
| ssoSegFunPerReg | ssoSegFunPerReg : starts segmentation of phase image and sets error flags |
| superSeggerOpti | superSeggerOpti generates the initial segmentation of rod-shaped cells. |
| systematic | systematic: Finds the minimum energy configuration by trying all segment |
| treeScore | treeScore : calculates the scores of regions/ segments using given classification tree. |
| watershedNoise | watershedNoise : uses watershed on an image and adds noise |
Master index