| ## Nuclei Segmentation | |
| ### Installation | |
| First, you can copy supporting plugins from this [directory](https://github.com/molonc/merFISH_report_pipeline/tree/main/imagej_macro/ImageJ_plugins/) into your `ImageJ/plugins/` folder. After that, your plugins folder will contains: utilities plugins at: `ImageJ/plugins/3D_suite`,`ImageJ/plugins/3D_viewer`,`ImageJ/plugins/utils`, and main plugin for this computation at: `ImageJ/plugins/spatial3dtissuej_plugin/TissueJ4Merfish_v14.jar`. Note: please use the latest package in this folder. | |
| ### Run scripts | |
| - Option 1: manual option: you can run macro by opening nuclei segmentation [macro](https://github.com/molonc/merFISH_report_pipeline/blob/main/imagej_macro/nuclei_segmentation/nuc_seg.txt) from ImageJ, and change input directory, input parameters and run macro. | |
| - Option 2: background mode, using [shell script](https://github.com/molonc/merFISH_report_pipeline/blob/main/imagej_macro/nuclei_segmentation/execute_segmentation.sh) to run program under background mode. See setting instruction in this file for different OS system. Note: java program will pop up a Java icon during the run, so program require X11 display syste, if you run this program from server, you need to install virtual environment xvfb-run in order to run it. See details in shell script. | |
| - Option 2: background mode. Similar to the second option above. But in case you have large number of input images, you can divide images into multiple folders, ex: 3 folders, and run shell script from each folder. Program will use multiple threads from your computer, so execution time will be much faster. | |
| ### Parameters | |
| - Nuclei segmentation: `minSize` minimum diameter of a nucleus, `maxSize` maximum diameter of a nucleus. Tell program that objects we expect are in this range. So program can work better. | |
| - `suffixe` usually .tif or .tiff. Tell program to scan entire folder to get the list of input files, and only file that ends with this suffixe will be taken into account. | |
| - `radius_max_cell_zone_extension`: for cell zone estimation step, from the periphery of a nucleus, extending into space with max radius to use as a cell membrane area. | |
| ### Testing dataset | |
| - You can run a testing example from this git repo first, before moving to your input images. See [Testing dataset](https://github.com/molonc/merFISH_report_pipeline/tree/main/imagej_macro/nuclei_segmentation/testing_images) | |
| - Output of nuclei segmentation for this testing dataset is at [directory](https://github.com/molonc/merFISH_report_pipeline/tree/main/imagej_macro/nuclei_segmentation/seg_results) | |
| - Output of ROI: region of interest, nuclei contours from segmented results will be at [directory](https://github.com/molonc/merFISH_report_pipeline/tree/main/imagej_macro/nuclei_segmentation/demo_results/). It helps to debug program, and see the performance of algo. Note: you can comment this function from bottom part of script if you don't need it [macro](https://github.com/molonc/merFISH_report_pipeline/blob/main/imagej_macro/nuclei_segmentation/nuc_seg.txt) | |
| - Output of cell zone detection will be stored at [directory](https://github.com/molonc/merFISH_report_pipeline/tree/main/imagej_macro/nuclei_segmentation/cell_zone_results) with two different formats: .tif and .zip. ZIP format is much smaller file compared to .tif. You can keep one only .zip format if you don't have space, and open .zip image from ImageJ. | |