Convert multiple z-stacks of different view into a single panoramic view with extended focus

Example workflow:

Instructions:

(1) Clone the repository

git clone https://github.com/duopeng/image_merge-z-stack_and_stitch

(2) Install dependencies

• Install ImageJ (tested with v1.53f51) or Fiji.
  Copy the two macro files focusstack.ijm and stitch.ijm to the macro folder in your ImageJ/Fiji installation folder
• pandas (tested with v1.3.3) and openpyxl

(3) Prepare an excel file containing the metadata

see metadata.xlsx for an example
The following picture shows an example that has two mosquito midguts (entities), and each gut has two microscope views (regions),and each region has 2 z-stacks.

(4) Prepare a folder containing images with names specified by the metadata.

The existing folder example_images contains the images for the example metadata

(5) Run the python script

python merge-z-stack_and_stitch.py --dir [path to image folder] --excelfile [path to excel file] --IJpath [path to ImageJ excutable]
To run the example:
python merge-z-stack_and_stitch.py --dir example_images --excelfile metadata.xlsx --IJpath [path to ImageJ excutable]

Result files will be named : [Entity prefix]_FocusStitch.jpg