alanaberdeen / aida Goto Github PK

Commit ab5148d.

I have some "rectangle" annotations in my files. So far, AIDA plotted them as intended, as rectangles with a black border and traslucent black filling. However, in this latest commit I've checked, borders appear white, and rectanngles have no filling. Example of annotation in .json file, and example of how AIDA is drawing rectanbles now (they don't necessarily correspond to each other). Note that I have placed the cursor within the rectangle so that AIDA selects it showing the border in blue, because the white border can barely be seen.

"layers":[{"name":"Blocks 0","opacity":1.0,"items":[{"type":"rectangle","class":"","color":{"fill":{"hue":0.0,"saturation":0.0,"lightness":0.0,"alpha":0.5},"stroke":{"hue":0.0,"saturation":0.0,"lightness":1.0,"alpha":1}},"x":9447,"y":5567,"width":2746,"height":2746,"locked":false},

Hi,

We have some new Zeiss .czi histology files. It seems that libvips does not support .czi to convert it to DeepZoom. I've put a .czi file directly in an AIDA images directory to see whether that worked by any chance, but when I go to the AIDA web interface and ciock on the file, it just loads a white image, so I guess it doesn't work. Do you guys have a preferred way to deal with .czi files?

Kind regards,

Ramon.

It seems that without specifying the limit for bodyParser.text() the error still persists.

Suggest to change to change this to

app.use(bodyParser.text({limit: '100mb'})

Hi @alanaberdeen ,

I think there's a bug here

I think the line should be

    "build:darwin:linux": "vue-cli-service build && cp -r aidaLocal/* dist",

Without the -r, when you do

npm run-script build

you get the error

cp: -r not specified; omitting directory 'aidaLocal/node_modules'
npm ERR! code ELIFECYCLE
npm ERR! errno 1
npm ERR! [email protected] build:darwin:linux: `vue-cli-service build && cp aidaLocal/* dist`
npm ERR! Exit status 1
npm ERR! 
npm ERR! Failed at the [email protected] build:darwin:linux script.
npm ERR! This is probably not a problem with npm. There is likely additional logging output above.

npm ERR! A complete log of this run can be found in:
npm ERR!     /home/rcasero/.npm/_logs/2020-07-22T23_41_57_261Z-debug.log
npm ERR! code ELIFECYCLE
npm ERR! errno 1
npm ERR! [email protected] build: `run-script-os`
npm ERR! Exit status 1
npm ERR! 
npm ERR! Failed at the [email protected] build script.
npm ERR! This is probably not a problem with npm. There is likely additional logging output above.

Hi, following the instructions in "Run locally" on Ubuntu 17.10. I get the error:

~/Software/AIDA/dist$ node aidaLocal.js
/home/rcasero/Software/AIDA/dist/aidaLocal.js:7
async function checkForImages () {
      ^^^^^^^^

SyntaxError: Unexpected token function
    at createScript (vm.js:56:10)
    at Object.runInThisContext (vm.js:97:10)
    at Module._compile (module.js:542:28)
    at Object.Module._extensions..js (module.js:579:10)
    at Module.load (module.js:487:32)
    at tryModuleLoad (module.js:446:12)
    at Function.Module._load (module.js:438:3)
    at Module.runMain (module.js:604:10)
    at run (bootstrap_node.js:383:7)
    at startup (bootstrap_node.js:149:9)

And when trying the "Develop" instructions, I get the error

~/Software/AIDA/dist$ npm run serve
npm ERR! Linux 4.13.0-46-generic
npm ERR! argv "/usr/bin/node" "/usr/bin/npm" "run" "serve"
npm ERR! node v6.11.4
npm ERR! npm  v3.5.2

npm ERR! missing script: serve
npm ERR! 
npm ERR! If you need help, you may report this error at:
npm ERR!     <https://github.com/npm/npm/issues>

npm ERR! Please include the following file with any support request:
npm ERR!     /home/rcasero/Software/AIDA/dist/npm-debug.log

Hi @alanaberdeen ,

Running AIDA locally, at http://localhost:3000/, I get the footballer's example image, with the example annotation.

Both the "Layers" and "Channels" panels have an eye icon that I though would hide/show the annotation. But clicking it doesn't seem to have any effect. The only way to hide/show the annotation is by using the slider in "Layers" to 0%. (The slider at 100% doesn't make the annotation fully opaque either).

I've created a .dzi file from an .ndpi with vips dzsave foo.ndpi foo, a fat histology slice. In the navigator, when using the Measure tool, it's giving me 0um for any measure line I draw. Not sure whether this is a known bug, or it's not implemented yet, or it has to do with my particular file, but just to let you know.

Hi @alanaberdeen ,

I suppose that the footballer's outline path in the AIDA example when running it locally is in file ~/Software/AIDA/dist/data/annotations/example.json, whereas the footballer's image is in ~/Software/AIDA/dist/data/images/example.jpg.

How are these two files connected? Just by having the same name (minus the extension)?

If I create a file ~/Software/AIDA/dist/data/annotations/foo.json and an image file ~/Software/AIDA/dist/data/images/foo.jpg, will they also be connected?

Hi,

This is a feature request that I though @ksirinuk could be interested in too. Say I have a lot of cells as path annotations.

Say we give each contour/polygon a confidence value from the segmentation algorithm. This value tells how sure we are that this cell is well segmented, that it's the type of cell we are interested in, etc.

The parameter can be added in the .json file as "cell_prob" \in [0.0, 1.0]

{"class":"","type":"path","color":...,"segments":[[61878.042394015,4476.5211970075],...],"closed":true,"cell_prob":0.7}

If AIDA had a slider that sets a threshold to only show path objects with cell_prob >= threshold, that would allow a human user to visually decide on a good threshold value.

Just pulled ab5148d, same data directory structure in ~/Software/AIDA/dist/data, but removing images.json that doesn't seem to be necessary anymore.

Interface with file browser in http://localhost:3000/dashboard shows both the annotations and images directories, and within images, both the .dzi file and its directory of auxiliary files.

Hi @alanaberdeen ,

I'm running AIDA on my desktop with

$ node aidaLocal.js 


Running AIDA at http://localhost:3000/

Let's say that the IP address of the desktop is x0.x1.x2.x3.

I have some image and annotations that display fine when browsing from said desktop, either http:localhost:3000/ or http:x0.x1.x2.x3:3000/.

However, if I browse http:x0.x1.x2.x3:3000/ from another machine, e.g. laptop, I still see the AIDA interface, but the Images page says "No data available".

Hi,

I've written a little function to convert Zeiss .czi files to DeepZoom .dzi using aicsimageio and pyvips (in my case, my interest is to be able to visualise them in the web browser application AIDA).

https://github.com/MRC-Harwell/cytometer/blob/c96e86c144c63978881330ad8275d10649096fcd/cytometer/data.py#L1525

The functionality is a bit limited to the Zeiss files I'm using now, and there may be a better way to do this, but I thought I'd drop a link here, as maybe somebody else is interested.

EDIT: I saw that others had the same issue.
Is it possible to fix this issue with a "patch" by replacing the "Rembrandt" image with my supplied image? I don't mind hard coding this change every time i need to annotate a different image (currently the annotations are only for my purposes, no users involved)

Thanks, and sorry for not reading other issues first

Hi,
First of all wanted to sat the editor seems very nice!
But i can't seem to upload an image for annotation..

The steps i took:
1)typed "yarn serve"
2)entered localhost:8080
3)clicked the settings logo, selected "Add an Image"
4)under source iv'e tried entering the file path to my image and even a url to a google drive image, under name i entered "bla"
5)clicked the "submit"

but nothing happened :(

what am i doing wrong?

In commit dd989e2, "Move Tool" with ~40,000 annotations, hangs up the interface. Just clicking on it, makes the interface freeze until you get a crash message.

Delete tool can only be used by selecting rectangles of objects to delete (just clicking on an object won't delete it).

How does one select an annotation object, by the way? Clickin on it doesn't work while the Lock View Tool is selected. Is it with the Move Tool?

Hello, after look through nearly 20 image annotation tools, I find your tool is the best! Especially your tool can draw curve easily, that's to say, we can annotate images by sylus! I clone your code and follow your instructions in issue#1, type npm run buildto build the project, then I run the commands below to check the project

sudo npm install -g serve
serve -s dist
but I got the pages

In fact, I want to get the project like your demo:

So how can I get the project run as your demo and annotate my own images? Can you give me some help? Thank you very much!

Hi @alanaberdeen ,

I think it'd be very useful to have on the bottom-left corner of the navigator the pixel XY coordinates of the mouse pointer. Then, that can be used to write down locations of interest for offline processing.

Maybe I can have a go at implementing that. Which file would that go in?

@alanaberdeen I'm summarising our email discussion here. It'll be more convenient.

The AIDA web server crashes when trying to delete cells and saving (It's a large .json annotations file, 290M). This happens, for instance:

• After annotations are loaded, simply by cliking the "Move" tool, the interface hangs up, and after a while, the browser (Chrome) reports that the page has crashed, and offers to reload it, which takes you back to the dashboard.
• After annotations are loaded, you can click the "Delete" tool, and delete annotations. But if you click "Save", the interface hangs up and then crashes as above.

A related issue is seeing significant lag panning/zooming around the image after the annotations are loaded.

Seen in commit 7b555aa

To reproduce the issue, open an image with annotations.

Click on an object, which selects it, and makes the filling transparent. Then click on another object. The first object gets deleted.

At least this happens when both object are overlapping with a third larger object that has the viewable switch off.

If after clicking on the first object you click on an area without any object in it, the first object gets deselected and not deleted, as expected.

Hi @alanaberdeen ,

Not sure whether this is related to issue #4 .

I'm running AIDA locally, on http://localhost:3000/, as per AIDA instructions.

In the starting page, I can see there's one image available, example.jpg. This image lives in ~/Software/AIDA/dist/data/images. As a test, I've copied this image with another name, foo.jpg in the same directory.

The initial menu doesn't see foo.jpg yet, after refreshing the AIDA starting page.

I assume the list of files is in ~/Software/AIDA/dist/data/images.json, which contains

["example.jpg"]

I've tried editing this file with different variations, and reloading the AIDA page, but none of these seem to expand the menu with the new foo.jpg file

["example.jpg", "foo.jpg"]

["example.jpg"; "foo.jpg"]

["example.jpg"]
["foo.jpg"]

How do I do this? On a related note, my files are .ndpi. Should I copy the .ndpi file to the images directory, or should I first convert to .dzi and then copy the resulting DeepZoom files?

Hi @alanaberdeen ,

System: Ubuntu Artful.

With AIDA current version 3816c9d, we have seen some interface bugs on a histology image with annotations. Namely, if I open the histology image on localhost with 1 layer of annotations, move the opacity slider below 100%, and zoom in, before reaching the highest zoom level, Chrome will freeze.

Only solution then is to kill the tab that's running AIDA.

We have also seen random non-reproducible bugs on remote browsing from another machine with Chrome and Firefox, where the annotations suddenly disappear when opacity goes below a threshold, or the image zooms in but the annotations don't, or they get a translation offset from their true position.

As long as the opacity slider is not touched, I don't seem to get those problems.

Hello, alanaberdeen,

Recently, I have been looking for an image labelling tool and compared a lot of image labelling tools mentioned in Wikipedia webpage. I found your label tool, AIDI, is outstanding and it suits me very well.
but this project seems to contain only the front-end part, and I wonder how I can deploy this tool on my server.
Any information would be appreciated.
thank you so much. ^_^

wulipc
2018-02-02 20:28:59