deepmicroscopy/exact

An open source online platform for collaborative image labeling of almost everything

exact's Issues

Optional automatic overlay of registered images

It would be so great to have the option to automatically (but optionally) load the registered image as an overlay after initial loading of the image.

Even more perfect, this would be built with an always visible slider, like this:

Provide REST API Calls for Online/Offline sync

Calls requested are:

• List products available in a dataset
• Add annotation type within product
• Remove annotation type (lower prio, just for completeness)
• Retrieve WSI

Install with Docker fails, because python version < 3.8

Hi I tried to install Exact using docker-compose, but it fails in the following step:

RUN pip3 install --no-cache /wheels/*

When it wants to collect the transformations package:

Collecting transformations
Downloading transformations-2020.1.1.tar.gz (44 kB)

I get a RuntimeError:

RuntimeError: Python version >= 3.7 required.

As the Dockerfile is using ubuntu 18.04 it is only using Python 3.6.9 which then fails the requirement

After prod Docker install: ImportError: Couldn't import Django. Are you sure it's installed and available on your PYTHONPATH environment variable? Did you forget to activate a virtual environment?

Hi,

I installed the prod version with docker-compose. It seemed to work fine. The log for the first command docker-compose -f docker-compose.prod.yml up -d --build can be found here: https://gist.github.com/Tyde/26a2bf733ecb5419bb4a1c20a50ed60e

When I try to run the second command: docker-compose -f docker-compose.prod.yml exec web python manage.py migrate --noinput I do get the following error:
Traceback (most recent call last):

File "manage.py", line 17, in <module>
    "Couldn't import Django. Are you sure it's installed and "
ImportError: Couldn't import Django. Are you sure it's installed and available on your PYTHONPATH environment variable? Did you forget to activate a virtual environment?

Docker build not feasible

Hi Christian,

the docker build does not work, there seem to be version missmatches. How could that be fixed?
I guess it is super easy :)

3.319 ERROR: Could not find a version that satisfies the requirement django-filter==23.2 (from versions: 0.1.0, 0.2.0, 0.5.0, 0.5.1, 0.5.2, 0.5.3, 0.5.4, 0.6a1, 0.6, 0.7, 0.8, 0.9.0, 0.9.1, 0.9.2, 0.10.0, 0.11.0, 0.12.0, 0.13.0, 0.14.0, 0.15.0, 0.15.1, 0.15.2, 0.15.3, 1.0.0, 1.0.1, 1.0.2, 1.0.3, 1.0.4, 1.1.0, 2.0.0.dev1, 2.0.0, 2.1.0, 2.2.0, 2.3.0, 2.4.0, 21.1)
3.319 ERROR: No matching distribution found for django-filter==23.2

Best regards,
CJ

Image annotation cannot be displayed correctly

@ChristianMarzahl I modified Python 3 running, allowed hosts, mapped IP, and tried local docker compose up-d. after success, I created and uploaded the image set, but the image could not be displayed correctly. The example is as follows.

Stack Image

It should be possible to superimpose two images with EXACT.
For example, two registered images.

How to run exact as server / allow access via the web?

Thank you again for this great tool!
How can I allow access via different IP addresses? Different to local host.
I tried to change the according line in the settings.py file to:
ALLOWED_HOSTS = os.environ.get("DJANGO_ALLOWED_HOSTS", default=['127.0.0.1', 'Bla.Bla.Bla.Bla']).split(" ").
However, it does not work.
On the web, there is this line often without os.environ mentioned to allow other hosts. However, this does also not work?

Previous/next image shortcuts not working with classification labels

When using classification labels, the previous/next frame shortcuts ((e) and (q)) are not working after one of the label checkboxes have been clicked.

OS: Windows
Browser: Firefox 85.0.2

Screening mode has stopped working

Apparently by introducing the rotation angle, the screening mode has stopped working.

The fault is in exact-image-viewer.js, where an undefined variable (rotation_angle) is being used in line 343.

It is fixed in the branch screeningModeFix.

Mouse wheel scrolls window and changes size of selected annotation

For small window sizes, scrollbars appear in the browser window.
When in annotation mode, using the mouse wheel then scrolls the window while also changing the size of the selected annotation.

Tested on firefox/ubuntu

Scale bar does not show up any more for non-WSI images

In the current (and the currently deployed version on exact.cs.fau.de) version, the scale bar does not show up any more for non-WSI images.

Demo Example: https://exact.cs.fau.de/annotations/297/

Internal Server Error (500)

Every time I want to create a new account, the internal server error (500) appears but when I want to register the account again, it shows the user name is already registered.

If possible, can you please delete the account with the user name "gu", "gu0923" and "gu1994"? Those are ghost accounts that I just created. Thanks.

Annotations being only partially saved if <enter> not hit

When adding rectangular annotations (only checked with those) within an image, these are only reliably stored into the database when "enter" is hit. While this is the intended workflow, the annotations are shown on the UI regardless if enter was hit or not.

In the following image, the left annotations were all clicked only a single time (and are shown all), without hitting enter at any time:

This is the result in the database:

Since the annotations are successfully shown, it is not unlikely that users deviate from the instructions and don't hit enter.

I would encourage to show annotations only after successful storage in the database (i.e. on server response), to have DB and UI always in sync, if this is not already the case.

Semi-blind mode for annotation

Hi, a useful feature would be a mode where I, as the administrator, could see the annotations of the various study participants, while the study participants would only see their own annotations.

Verification skips images

Hello Christian,

I think I found a small bug in the annotations verification. Sometimes when I click verify on an image to complete my annotation, it is not saved. If I then select only unverified images to display, those which I have previously verified are also displayed. Also, some images are displayed as both verified and unverified. The error occurs on images where no objects have been annotated. However, not all images on which no objects are annotated are overlooked.

Kind regards
Jonathan

Wrong link in README.md

The following link does not/no longer work:

Our production uwisgi config can be found at https://github.com/fsinfuhh/mafiasi-rkt/blob/master/imagetagger/uwsgi-exact.ini

JavaScript crashes when subtracting polygons

When trying to subtract two polygons form the same class from each other a JavaScript error accours.

Incorrect display of images

When I am opening images in the application to label them they appear a bit strange. I added a screenshot of the correct image and the incorrect one.

Attached you can find the .png file.

An exception if Annotation Type already existed.

An exception can’t be handled when creating a new Annotation Type if the name already existed.

"
In fact, it will be more reasonable to allow the creator to delete every unused annotation type, which are not used in any ImageSet.
"

Image classification key maps inverted

When labelling a classification dataset with two classes, the key mapping for assigning the classes is displayed as Shift-1 and Shift-2. However, Shift-1 assigns the second class, while Shift-2 assigns the first one.

Thumbnail not deleted -> registration problems after reupload

When an image is deleted (tested from the API), the thumbnail image still resides in the file system.

This leads to the following chain of errors:

• When uploading another image with the same filename, the new thumbnail is not being generated (as it already exists)
• When trying to register this new image (which utilizes the thumbnail apparently), the registration fails.

Steps to reproduce:

• Upload an image (e.g. 1.tiff)
• Delete the image
• Finding 1: 1_thumbnail.png still resides in the data directory
• Upload other image with same filename (1.tiff)
• Finding 2: 1_thumbnail.png was not updated.

In Exact/images/api_views.py:478 the destroy() routine also does not include removing the thumbnail.

BugFix Enter

Trouble with installation on Ubuntu

First of all, thank you very much for this excellent tool.
Unfortunately, I have trouble installing it on a Linux machine (Ubuntu 22); not due to the Ubuntu version.
I have cloned your repo, modified the env files in the subfolder exact/exact, and then started the installation via:
sudo docker-compose -f docker-compose.yml up -d --build
By doing so, there is an error with a requirements.txt file. I have copied that one from the subfolder exact to the main folder.
However, there is still this error:
The command '/bin/sh -c pip3 install -r requirements.txt' returned a non-zero code: 137
ERROR: Service 'web' failed to build : Build failed

Menubar dropdowns only work on "Home"-Page

Correct behaviour:
Open "Home"-Page
Click on "Administration", "My Teams", "My Profile" --> The dropdown menu is displayed

Expected to work on any other page as well:
Open "Explore"-Page, "Administration", "My Teams",...
Click on "Administration", "My Teams", "My Profile" --> No dropdown menu is displayed

Shortcuts for previous/next frame

It would be lovely as well to have keyboards shortcuts for previous/next frame.

Creation of datasets based on references to an existing dataset

Currently there are issues when a dataset is created, where the images are references to existing images that are already on the EXACT server. The current solution is to copy the images, what requires more memory on the server.

Mp4 Support

Besides AVI, MP4 should be supported

TypeError while screening

From console output:

Uncaught TypeError: cv.Mat is not a constructor
matFromImageData opencv.js:30
imread opencv.js:30
updateThumbnail screeningTool.js:160
jQuery 8
initUiEvents screeningTool.js:91
getHandler eventsource.js:162
raiseEvent eventsource.js:184
success exact-sync.js:128
jQuery 6
loadScreeningMode exact-sync.js:119
EXACTScreeningModeSync exact-sync.js:114
ScreeningTool screeningTool.js:15
EXACTViewer exact-image-viewer.js:28
factoryCreateViewer exact-image-viewer.js:143
displayImage exact-imageset-viewer.js:190
imageSetInformationLoaded exact-imageset-viewer.js:105
success exact-sync.js:292
jQuery 6
loadImageSetInformation exact-sync.js:262
EXACTImageSetViewer exact-imageset-viewer.js:18
annotations.js:38
jQuery 13
opencv.js:30:7673291

Error when creating an ImageSet in the web api

When trying to create a new ImageSet via the web api an error occurs and the ImageSet is not created.
Creating a ImageSet with the Exact-Sync api works.

The server is running on Windows with Docker.

Safari Annotations

Reminder: Known issue with Safari annotations and BroadcastChannel

Filled Polygons

Hello Christian,

it would be really cool if Exact could offer the possibility to visualize annotations as filled polygons.
Thank you for your great tool!

Kind regards
Frauke

Cannot add annotations in "full page" (fullscreen) mode.

When switching to "full page" (fullscreen) mode using the beveled round "Toggle full page" button, it is no longer possible to add annotations, even when "c" is pressed on the keyboard or annotation mode is on before pressing the button.

(tested on chrome, firefox and safari on ipad)

Feature suggestion: Encoding slide/frame id in url

For volumetric/time-series data, it would help communication to encode the slide/frame id in the url itself (as is currently implemented for x & y coordinates).

Error message on deleting images

When deleting an image in annotation mode, the URL is not updated, thus you can receive an error 404:

Page not found (404)
Request Method: | GET
Request URL: http://127.0.0.1:8000/annotations/4/
Raised by: exact.annotations.views.annotate

Feedback for Exact from Bio-Totem

Thanks for your improvement on this collaborative online platform project. We find it very useful after a few days of trial on the platform. However, we believe that if you can improve the functions listed in mail attachment(which was send form [email protected]), the platform would be more popular.
Thanks

Exception when last action image was deleted

When the image shown in last_action was deleted, it is no longer possible to use exact, since there is an error immediately after login:

django.urls.exceptions.NoReverseMatch: Reverse for 'team' with arguments '('',)' not found. 1 pattern(s) tried: ['users/team/(\d+)/$']

Most likely, the team of the image can no longer be looked up, which causes the error.

Tried a lot to figure out the error but couldn't

Plygon is not connected as a contour

I'm now using polygon to annotate for segmentation map, but I find sometimes the start point and the end point of the polygons are not connected.


The first image shows my annotation on the Exact server. The second image shows the annotation that I downloaded from the server.
This error can be reproduced when the starting point and end point of the polygon are too far away from each other.

Usability DetailViewer

For optimal handling of the planned DetailViewer, it would be great to

• be able to de-/activate it with a Keyboard-Shortcut OR a button in the taskbar (you could use the "magnify" material design icon available at https://materialdesignicons.com/ ).
• toggle between the main-viewer and the detail-viewer via keyboard shortcut
• highlight the frame around the detail-viewer whenever it is active (toggled) and display a pointer to the original location in the main-viewer (as displayed in green ... maybe not the best choice in color ;-) ) as displayed below. This pointer would need to adust its location whenever the user navigates within the detail-viewer.

Happy coding :-)
Christine

Adaptions to mainland China or VPN

"Loading Images is difficult for users running this platform in a private network without internet connection, or users in mainland China, who are unable to access URL that you use in the html file mentioned above without VPN. I am not quite sure why online URL addresses are necessary, but it will make the platform more friendly if changing online URL into local paths in this html file"

Creation of images directory required.

Just tried to install Exact on a fresh instance from the README, and apparently it required the creation of the "images" folder in Exact/exact/images before running the migration.

I think a fix will be to just add an empty folder to github so that this will be created automatically, or to add it to the README.

Collaboration among groups of people

Hi I have accessed the EXACT label Server. A collaborator and I want to label some images. But we cannot find a way to allow the other into the set to collaborate. Is there a guideline for that?
Thank you, and your work is great

Provide shortcuts for frame-based (global) annotations.

To enhance annotation speed it would be lovely to have keyboard shortcuts for global annotations.

Error Launching Exact with Docker Compose File

Having an issue launching Exact in Docker.

Using Docker Desktop for Windows 10
Clone GIT Repository
Run following command from CLI in repo folder: docker-compose -f docker-compose.yml up -d --build

Container is built successfully, but get following error when it starts. Any help would be appreciated.

ERROR: for web Cannot start service web: OCI runtime create failed: container_linux.go:349: starting container process caused "exec: "/usr/src/exact/entrypoint.sh": stat /usr/src/exact/entrypoint.sh: no such file or directory": unknown
ERROR: Encountered errors while bringing up the project.

Stroke resets when moving within one scale level

The thickness of lines can be changed through the stroke slider, but resets when the image is moved, even without changing the zoom level.

cannot make sync work

Hi,
I am trying to use the sync option to visualize two images at the same time. But when I click to look for other images it doesnt show anything:

In your image registration video it shows you an ihc image right away. Am I missing some step?
Thanks!