hdr_project

Overview

hdr Matlab implementation with fluorescence imaging

Code based on https://www.researchgate.net/publication/327545585_Deep_dive_into_high_dynamic_range_imaging_a_Matlab_tutorial DOI: 10.13140/RG.2.2.30129.43365 Adapted for green channel fluorescence imaging and image segmentation

Save the Original Images

All images will be saves in the Originals folder which is a folder in the hdr_project directory

1. Create a folder with your project name inside the Images Folder besides the AllChannels Folder. This will help to easily save the segmented images in the right place and to retrieve the right images.

2. Create a subfolder called "Originals"... IMPORTANT NOTE: This folder should contain ONLY the images you want to analyze and no other files. The code will not work if there are other files in this folder.

3. Rename all your images with the proper convention (see 'File naming convention' section below) IMPORTANT: If you don't input this correctly the exposures will be read incorrectly and the values the algorithm will output will be incorrect.

File naming convention

Each file should be labeled as such:

'imageName_numerator_denominator'.filetype

Numerator and denominator correspond to the numerator and denominator of the exposure of that image. For example, a tif image with an exposure of 1/4 should be named 'im_1_4.tif' Additionally, neg4 will have an exposure of 1/4, neg5 will have an exposure of 1/8 and neg6 will have an exposure of 1/15.

imageName cannot contain any numbers. Please use the folder name to specify the series of images.

Images Folder Structure

Include all ldr images in a folder. You cannot have a folder and standalone images in one folder. Make sure the folder you are taking images from ONLY has images. The code will ignore .DS_Store files files names '.' and '..'

Please do not include any other files in the folder with ldr images.

How to Run the Code

1. Open setup.m and follow the instructions to run each block one at a time
2. Run HDR_main.m
3. Output will be saved in as hdrMap and further normalization might be necessary before saving your files. The code will automatically generate a folder next to your original images folder with a hdrMap saved in it. It will be normalized by the maximum value of all the channels.