{:title "Next_image_clj: a simple utility plugin for semi-automated analysis" :date "2019-12-31" :updated "{{{time(%Y-%m-%d %a)}}}" :tags ["clojure" "imagej" "Fiji" "programming" "science"]}

Next_image_clj: a simple utility plugin for semi-automated analysis

First published: 2019-12-31 Wed
Last updated: 2019-12-31 Tue

Often I have large directories of images that I want to analyze in with some ImageJ plugin or script in a semi-automated manner. For example, recently I wanted to measure the fluorescence intensities of a few different regions of interest (ROIs) I had traced on a microscopy image. I wrote a python script which would measure the area of each ROI and save the values in a specially designed CSV to facilitate later analysis. My workflow was simple:

Manually tracing and renaming ROIs is enough work, clicking and dragging images around the desktop makes an already tedious task even more so. Eventually, I wrote a function at the end of my script that would close my current image, move it to the done directory, open the next one, and print out how many images were left to analyze to the imageJ log. This made things a lot easier and nicer, and I decided to generalize this functionality to a plugin.


ImageJ/Fiji plugins are primarily written in Java. I've never written a bonafide plugin (only Jython scripts that act like plugins), and I have very little experience writing Java. I have been learning about and playing with Clojure for over a year now, and I thought it would be a good opportunity to try implementing this basic plugin with Clojure.
Eventually I want to learn a bit of Java by rewriting this plugin and I will document that experience as well.

Next_image: a tool for manually analyzing large image datasets

So what will the Next_image plugin do?
Next_image will ask for a directory upon startup, and will then list all the images in that directory. It will expect the images to exist together in some main directory, and already-analyzed images (and their associated data) will reside in a directory called done.

├── done
│   ├── imgXdone.tif
│   └── imgXdone_data.csv
├── img1.tif
├── img2.tif
└── img3.tif

If this directory tree doesn't exist yet, Next_image will create it in the selected directory. I think we will also make a .next_image_state file to hold the state between analysis sessions.

Next_image is meant to assist with semiautomated analysis. You will have the option to register custom pre-processing and post-processing macros or scripts which will be run immediately after opening an image (pre-processing) and before closing the current image and opening the next (post-processing). Next_image will display a list of the images in the main directory, and will have a button (called next) to load a selected image or move to the next. If no image is open, Next_image will open the selected image and run the pre-processing macro. Upon clicking the button (or triggering with a keyboard shortcut), Next_image will open the image and run your pre-registered pre-processing script. You will then be left alone to analyze the image however you see fit. When you are done, click next and Next_image will run your registered post-processing script, close the image, move it to the done repository, open the next image, and run the pre-processing script.
And that's it, that will be the main functionality of Next_image. The user interface will display a list of the images left to analyze, tell you how many are left and what % of the total they comprise, and how many you have analyzed so far in this session.

I am still working out the GUI layout, but I will update this page as I work on the application. You can also find the code on github. Again just a warning that this is my first plugin (and serious clojure project) and I am learning as I go.

It is new years eve (2019), so I'll work on this more tomorrow. Check back soon for updates and explanations of the code (and happy new year)!