plugins/macros for ImageJ/Fiji
- File conversion
- Visualisation 3D
- Align stack
- Select specific Rois
- Correct bleaching
- Ellipsoid 3D (fit, measures)
- LOCO EFA (shape complexity)
- Curvature (unsigned curvature)
- Moran index (spatial auto-correlation
- Cortex segmentation (from cortex marker)
- Radioak plugin (radius)
- Local texture (GLCM)
Macros to automatically convert a batch of files.
convertCZIto8bTiff.ijm: convert all .czi files in a folder to .tiff format, and 8-bit type if selected.
Visualisation of 3D stacks.
Center and rotate each slices of a stack based on image moments so that they will all get the same average position and orientation (global alignement). Works best on binary images. On non-binay images, adding weight to positive pixels (noise reduction option) helps to be less sensitive to background pixels, otherwise, highly biaised.
When there are several Rois by z-slice, select only one "best" Roi for each slice. For example, select for each z-slice the Roi that have the highest area among all Rois that are present in each z-slice. Delete the non-selected Rois.
Keep all Rois that have a desired property (e.g. circularity between two given values, orientation (angle of the Roi main direction) between two specific values.. ).
Correct bleaching in a 2D temporal stack by histogram matching. Match all histograms to the first slice. Usefull for segmentation afterwards.
Handle 3D ellisoid operations. From a binary stack, calculate the 3D ellipsoid corresponding to the positive pixels. Print its characteristics: centroid position (Xc, Yc, Zc), semi-axis lengths (A, B, C), volume, and eigen vectors (axis directions) (vA, vB, vC). Draw the 3D ellipsoid on the input image for visualisation of the fit.
Measure characteristics of the shape complexity with the LOCO-EFA method (lobe contribution elliptic Fourier analysis), defined in Sanchez-Corrales et al. (2018). Reconstruct the shape with 2 to 50 modes as Roi, and calculates the contribution mode, distance between the shapes and entropy of the shape.
Calculate unsigned curvature along a ROI.
Calculate Moran index (Moran 1950) on first Roi in RoiManager, with weights being 1 if pixel j inside k-neighbors of pixel i (k is a user defined parameter), 0 otherwise.
Segment cortex from fluorescent marker stack. Look at local maxima on each angle around the center.
Extract the values of the radius of a given Roi at n angles around its center. Allows to quantifiy the shape fluctuations. Offers option to visualize these dynamics.
Calculate one of the GLCM textures in a moving window of a given size. Output a new image with the value of the chosen texture in each of the moving window. Windows move with step size in x and y of the parameter step, and calculate the texture in a neighborhood of given size.