Calculation of Sensitivity and Specificity for Enhancer-based images
- Requires MATLAB 2022b+
- Clone the repository
- Create two folders: OPR_img, OPR4
- Download the JAR package and place it in the folder
- Add to the path the folder bfmatlab, with its sub-folders
- Download the folder for pre-processed channel-wise images Download image
- Conversion of Bio-format images to separate channels
- Optional; if you have not downloaded the channel-wise images as stated above
- Lines 6-14: perfov: Enhancer-Marker combination (only one should be uncommented)
- Line 15: Individual Filename
- Lines 49-52: Uncomment for Double Enhancer only
- Lines 123-125, 137, 141, 146, 150: Uncommnet for single enhancer (Comment Lines 127-136, 139-140, 144-145, 148-149)
- Lines 127-136, 139-140, 144-145, 148-149: Uncommnet for double enhancer (Comment Lines 123-125, 137, 141, 146, 150)
- Certain special heuristic pre-processing parameters are mentioned in the comment for some images; uncomment accordingly
- Detection of Cells marked across each Channel by Morphological techniques
- Input Folder: OPR4_img containing the channel-wise images downloaded above (or generated above)
- Ouput Folder: OPR4 containing Cell-cemeters of detected cells and detection overlayed on the image channel
- Lines 6-20: perfov: Enhancer-Marker combination (only one should be uncommented)
- Lines 46-123: Detect cells marked by enhancer1 in case of double enhancer or single enhancer (Uncomment only one code block corresponding to the Enhancer-Marker combination)
- Lines 125-167: Detect cells marked by enhancer2 in case of double enhancer (Uncomment only one code block corresponding to the Enhancer-Marker combination)
- Lines 170-242: Detect cells marked by marker (Uncomment only one code block corresponding to the Enhancer-Marker combination)
- Lines 244-298: Detect cells marked by DAPI (Uncomment only one code block corresponding to the Enhancer-Marker combination)
- Certain special heuristic morphological parameters are mentioned in the comment for some images; uncomment accordingly
- Prerequisite: Run ug3_enhcSpecTest_Samik_New.m to get Detection CSVs
- Calculation Specificity and Sensitivity according to detected cells
- Lines 6-20: perfov: Enhancer-Marker combination (only one should be uncommented)
- Line 35: Uncomment for single/double enhancer (Comment Line 36)
- Line 36: Uncomment for double enhancer
- Output: Array sens[] for all samples for sensitivity, Array spec[] for all samples for specificity