Focus Annotator - a tool for annotation the focal plane of a part of an image

Related tags

Image processing rust microscopy z-stack data-annotation focus-stacking
Overview

Focus Annotator

Focus Annotator is a tool for annotation the focal plane of a part of an image. It is a tool I built in rust as part of my master's thesis to make image focus annotations for z-stack images quicker.

image

Installation

You can either download the latest release here or compile from source.

Compilation Instructions

Docker

The tool can be compiled with docker-compose:

  • Linux Version docker-compose up (compiles to AppImage)
  • Windows Version: docker-compose -f docker-compose.windows.yml up (the resulting file is packaged as package.zip, dependencies included)

Native

The prerequisits can be installed as described in the gtk4-rs book:

After the prerequisits are installed you can run/build the tool as is usual for rust:

cargo run

Usage

When opening the program open a .json file that describes where to find the images. The file should look as follows.

[
    {
        "images": [
            {
                "image_path": "img/30_753da05d-cd1e-45c5-8593-003323e0bb69_I00243_X013_Y003_Z4648.jpg",
                "neighbours": [
                    "img/30_753da05d-cd1e-45c5-8593-003323e0bb69_I00243_X013_Y003_Z4648.jpg",
                    "img/30_753da05d-cd1e-45c5-8593-003323e0bb69_I00243_X013_Y003_Z4648.jpg",
                    "img/30_753da05d-cd1e-45c5-8593-003323e0bb69_I00243_X013_Y003_Z4648.jpg",
                    "img/30_753da05d-cd1e-45c5-8593-003323e0bb69_I00243_X013_Y003_Z4648.jpg",
                    "img/30_753da05d-cd1e-45c5-8593-003323e0bb69_I00243_X013_Y003_Z4648.jpg",
                    "img/30_753da05d-cd1e-45c5-8593-003323e0bb69_I00243_X013_Y003_Z4648.jpg",
                    "img/30_753da05d-cd1e-45c5-8593-003323e0bb69_I00243_X013_Y003_Z4648.jpg",
                    "img/30_753da05d-cd1e-45c5-8593-003323e0bb69_I00243_X013_Y003_Z4648.jpg"
                ]
            }
        ],
        "best_index": 0
    }
    {
        "images": [
            {
                "image_path": "img/31/I03987/I03987_X008_Y026_Z5498_0_1200.jpg",
                "neighbours": [
                    null,
                    null,
                    null,
                    "img/31/I03987/I03987_X008_Y026_Z5498_0_1125.jpg",
                    null,
                    "img/31/I03987/I03987_X008_Y026_Z5498_75_1125.jpg",
                    "img/31/I03987/I03987_X008_Y026_Z5498_75_1200.jpg",
                    null
                ]
            },
            {
                "image_path": "img/31/I03988/I03988_X008_Y026_Z5566_0_1200.jpg",
                "neighbours": [
                    null,
                    null,
                    null,
                    "img/31/I03988/I03988_X008_Y026_Z5566_0_1125.jpg",
                    null,
                    "img/31/I03988/I03988_X008_Y026_Z5566_75_1125.jpg",
                    "img/31/I03988/I03988_X008_Y026_Z5566_75_1200.jpg",
                    null
                ]
            },
            {
                "image_path": "img/31/I03989/I03989_X008_Y026_Z5703_0_1200.jpg",
                "neighbours": [
                    null,
                    null,
                    null,
                    "img/31/I03989/I03989_X008_Y026_Z5703_0_1125.jpg",
                    null,
                    "img/31/I03989/I03989_X008_Y026_Z5703_75_1125.jpg",
                    "img/31/I03989/I03989_X008_Y026_Z5703_75_1200.jpg",
                    null
                ],
            }
        ],
        "best_index": null
    }
]

The json file contains a list of unamed objets. Each object corresponds to one focus stack. Best index is set to null for non annotated images and is a number corresponding to the image in focus once annotated. The array image present in each focus stack contains objects tat represents the individual images.

Each individual image has an image_path (mandatory) which is relative to the position of the json file, and 8 (!) neighbours (which are allowed to be set to null). Neighbours are represented indexed the following way:

0 1 2
3 - 4
5 6 7

You are allowed to store additional data in focus stack objects (and image objects) and this should be preserved when using the tool, however, make sure to back up the metadata file before using the tool.

Keyboard shortcuts

The tool supports keyboard shortcuts:

  • w - move up in the focus stack
  • s - move down in the focus stack
  • b - back - go back one image
  • n - next - skip image
  • m - mark - mark current image in the z-stack as in focus and go to next image

Contributing

Pull requests are welcome. For major changes, please open an issue first to discuss what you would like to change.

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Comments
  • Opening a file on windows crashes the program

    Opening a file on windows crashes the program

    Possibly this is an issue related to joining of paths as it gives the following error:

    "stream did not contain valid UTF-8", src:main.rs:110:73
    bug windows 
    opened by 13hannes11 1
  • Opening another file causes a panic

    Opening another file causes a panic

    This is most likely due to the ways state currently is kept in the program. A cleaner way would be to use a separate thread that manages the state and is communicated to by using channels:

    A channel example from this blog:

    use rand::Rng;
use std::{collections::HashMap, sync::mpsc};

fn do_work(tx: mpsc::Sender<u64>) {
    let mut rng = rand::thread_rng();
    for _ in 0..100_000 {
        let key: u64 = rng.gen_range(0..10);
        tx.send(key).unwrap();
    }
}

fn main() {
    let mut m: HashMap<u64, u64> = Default::default();

    crossbeam::scope(|s| {
        let (tx1, rx) = mpsc::channel();
        let tx2 = tx1.clone();
        let m = &mut m;

        s.spawn(move |_| {
            while let Ok(key) = rx.recv() {
                *m.entry(key).or_default() += 1
            }
        });
        s.spawn(move |_| do_work(tx1));
        s.spawn(move |_| do_work(tx2));
    })
    .unwrap();

    println!("map = {m:#?}");
    println!("sum = {}", m.values().copied().sum::<u64>());
}
    bug 
    opened by 13hannes11 1
  • CICD avoid running twice on tagged commits

    CICD avoid running twice on tagged commits

    This can be done by either only running on tags to build a release or by having separate actions.

    Not doing this can result in issues regarding artefact uploads when the tag is pushed at the same time as the original commit.

    CI/CD 
    opened by 13hannes11 0
Releases(v0.1.1)
Owner
Hannes Kuchelmeister
Student at Uppsala University
Hannes Kuchelmeister
GitHub
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