And so the last opened projects are no reloaded.

I installed cytomine bootstrap in vmware with linus ubuntu server, i also installed cytomine web ui in both windows and vmware, now i have no clue what to do

you can help me? thank you

Hello,

I have noticed that the "review layer" is invisible. It also bugs out the annotations in the other layers when it is set on visible.

In addition, in the annotations tab, it is impossible to switch to the reviewed annotations (the manual and algorithm annotations options work normally).

These errors were observed on the cytomine cloud app.

Current :
To deplace the viewport, you can use the minimap in the following way :
“drag the view box in the area that you want to display”

Wanted :
A simple "click" on the new targeted view is simplier.

I have followed the installation instructions for Cytomine 3.0.0 at https://doc.cytomine.org/How-to-install-Cytomine, and I selected option (b) "make your Cytomine instance accessible from other computers." I have the URLs section of the configuration.sh file set as follows (with [my-domain] replaced with the domain name I'm using).

CORE_URL=[my-domain]
IMS_URL1=[my-domain]/ims
IMS_URL2=[my-domain]/ims2
UPLOAD_URL=[my-domain]/upload

It's not clear to me from the documentation what the user name should be, so at the log in page, I tried 'admin' and entered the password from the configs/core/cytomineconfig.groovy file. When I click the 'Log in' button, the browser sends a POST request to http://[my-domain]/j_spring_security_check, but the response from that POST includes the following redirect header:

Location: http://localhost/login/authfail?ajax=true

Going to 'localhost' cannot work, of course, because the browser is running on one machine and the Cytomine software is running on another.

I've been looking through several of the related docker containers to see why 'localhost' is being sent instead of the domain name I selected, but thus far, no luck.

Can you offer a suggestion that might help?

Thanks much.

When creating a new user in Cytomine, the form says : "Must have at least 4 characters" but actually it's 8 characters
logs: "Your password must have at least 8 characters!"

Currently, the Web UI ask for the fetching of all the annotation classified by a defined category (user, term, etc.)

This PR (#89) set a limitation of the number of categories to avoid backend flooding.
However, this is a strict limitation and missing annotations would only be fetch by a more precise filtering (remove some terms or users).

I think it would be a nice feature to

• don't flood the backend;
• be able to see everything :-)

I see 2 options :

• An "hot loading" : only load the annotations related to the first categories then load the next if the user scroll down;
• Load all categories with only the number of annotations (dedicated api request) and by extending the "category row", load the related annotation

Maybe there is other options that I don't see at this moment.

In a project, when working on an instance used for years, we can have a difficulty to load the annotations.

In the ListAnnotations file, we load all the users. In some instances, the users are numerous and this request take more than 5 seconds (more if the instance is massively used at this time).
The panel stay unavailable with the loading wheel.

The users are used in the AnnotationDetails component to display the creator or reviewer of this annotation.
But currently, if a creator is removed its annotations are no more displayed.

When I reload a viewer into my browser,
(url is BASE_URL/#/project/P/image/I1-I2-I3?viewer=V )

the order of the opened images is not kept. It can be disturbing for the user.

Attended behaviour :
The image order is kept.

The following screenshot shows an RGBA image where the black background has an alpha of 0.

When zooming in, the background changes to white.

I have also tried to disable the Digital Zoom, the issue persists.
Although this is shown on the ULiège instance, the bug was reproduced by Ba Thien on another instance.
I can send the image (<100kB), if needed to reproduce of the bug.

I have a question. Open cytomine viewer the images in dicom wsi
Format or it opens propietary images from scanners?
Kind regards and thank you in advance.

Currently, the search is made independently of the terms.

If we unselect a term, we still ask back-end to search for all annotations (including this term) and mask them.

1. It will be better for performance to search for the displayed terms.
2. A consequence is that for clusters, the count is "false". We display the number of all the clustered annotations including the masked one... Even if we ask to see only one term with few annotation (and in this case, a cluster is not to display (i.e. the back-end will not return the cluster information)).

When I try to launch a Job with optional parameter with no default value, I got the message
Failed to launch the analysis

It is coming from the line
https://github.com/cytomine/Cytomine-Web-UI/blob/master/src/components/job/AddJobModal.vue#L136

If this value is approved by the back-end, the front-end must let the null values pass.

Hello,

I have some issues regarding cytomine development setup. I have made the regular installation of cytomine core on local machine. It is working fine. For the front end I have installed cytomine-web-ui as follows:
Hello,

I have some issues regarding cytomine development setup. I have made the regular installation of cytomine core on local machine. It is working fine. For the front end I have installed cytomine-web-ui as follows:

The issue I am having is that in the cytomine-web ui, I can see the projects created in the cytomine core but could not open them, it says ‘the page could not be found’. Moreover I am unable to create a project or upload the images.

In the configuration.sh file, if I make the parameter Core-development to true and run it, both cytomine core and web-ui shows the login screen but when I try to login it says ‘Unexpected Error Occured’.

In the configuration.sh file, if I make the parameter Web-Ui or IMS-development to true and run it, cytomine core gives the error of Bad gateway but cytomine web-ui works fine. I am able to create projects and upload images but in this case, the issue is that when I try to open some image, it says ‘failed to fetch annotation layers’ and the image could not be opened.

Kindly help me with this.

When uploading a seemingly faulty image and triggering an error on the IMS (e.g. cytomine/Cytomine-IMS#33 or other errors of the java.lang.Exception: Openslide is unable to read nature) either the upload status is stuck at "Detecting format" or "Deploying", but without any error message visible to the user.

Please forward the error to the UI.

Failed to compile.

How i resolve this error? ... after i type this in browser: http://localhost:8080/

./src/components/admin/AdminUsers.vue
Module Error (from ./node_modules/eslint-loader/index.js):
error: 'getWildcardRegexp' is defined but never used (no-unused-vars) at src/components/admin/AdminUsers.vue:117:9:
115 | import UserDetails from './UserDetails';
116 | import {rolesMapping} from '@/utils/role-utils';

117 | import {getWildcardRegexp} from '@/utils/string-utils';
| ^
118 |
119 | export default {
120 | name: 'admin-users',

1 error found.

Hi @geektortoise, @urubens and Cytomine developers,

We're doing collaborative analysis with the pathologist, on the analysis annotations (nuclei detection and classification). There are some features related to annotation work which we think would be useful or can be improved:

1. To edit the analysis annotation terms when the Review stage is enabled.
2. To enable/disable colour overlay of the annotations without affecting the outlines.
3. To change annotation outline colours for each term. So that when we disable colour overlay, we can still distinguish the different annotation terms
4. To enable "Correct annotation by adding a freehand area" and "Correct annotation by removing a freehand area" tools for analysis annotations. These are very useful because the pathologist don't have to edit each point using "Modify" tool.
5. "Fill" tool has unclear usage. I have tried using it several times but it did not capture anything.

I went through the documentation and could not find further info on these. We would like to ease the pathologists work as much as possible hence we look forward to getting your response.

Thank you very much

.

Currently the implementation of the .navbar-item.has-dropdown class in src/components/navbar/NavbarDropdown.vue relies on toggling the .is-active class which works fine on Chrome and FireFox, but not on Edge.

The Bulma docs provide an example that adds the .is-hoverable modifier to the .navbar-item.

It would be a nice feature to be able to select multiple annotations.
Example :
Click on one annotation -> Display of the annotation details
MAJ + click on another annotation -> Hiding of the annotations details (there is no more "THE current annotation" to show)
Two annotations are selected
Then when click on delete, we should be able to delete the 2 annotations with a single "confirm" (one confirmation pop-up for all the annotation deletion) => The message should vary and contains the number of annotation to delete.

ULiège made this PR :
#100

In my conception, it would be better if the developer mode is set in the "admin" section instead of the "my account" page.

When changing the brightness / contrast / etc - the changes are not persisted and the viewing is a little choppy because tiles are first shown THEN adjusted through brightness / contrast / etc .

If possible, would be better to first pass any tile(s) through the brightness / contrast / etc changes before being presented on the screen

When .svs images are displayed at lower magnification levels, they appear to have faint grid lines. I do not see these line when the magnification is increased to 5x or higher. The lines appear whether or not digital zoom is on. These lines don't appear when the image is in .ndpi or .jpg format. The images below are from screenshots of the browser taken at different magnification levels.

Magnification 0.63x

Magnification 1.25x

Magnification 2.5x

Magnification 5x

Hi,

I was adding new users to 3 existing projects, and configured the download permission for each project as ''Images downloadable by contributor'. After doing these, there seems a few problems with the Projects page:

1. One of the projects disappeared from the Projects page
2. Total number of images for the other 2 projects became lesser (from 37 to 0, and from 171 to 6)

The missing project and images are still there, accessible from "Recently Opened". Maybe there is a bug somewhere. Our Cytomine was already updated (core v3.0.3).

Hope to get this sorted out to avoid confusion to our collaborators when seeing the missing project and images. Thank you.

Recently Opened panel showing "ER WSI" project:

Projects page has no "ER WSI" project:

Project "ER Patches" still has 100+ images, but only showing 6 in the project information:

Some problems appeared with annotations.
Example : each time I close the information pop-up, it opens again.

It seems that it is caused by the package-lock.json update and the vuelayers version evolution from 0.11.4 to 0.11.22.

When I force version 0.11.4, it works fine.

Pathologists use the slide label for identification of the patient/staining; displaying the slide label would increase confidence in using cytomine.

Label images are served by the backend:

$HOST/api/imageinstance/$ID/associated/label.png

or

$HOST/api/abstractimage/$ID/associated/label.png

Please include the label in the accordion chevron-cell near "Slide preview" and on the image viewer.

An alternate view-mode incorporating this feature could look like this:

Allow an export of the current view of the image.

As spotted by @anttikos here :
cytomine/Cytomine-core#1179

It is currenlty impossible to select an annotation behind another one.
If the fix will allow us to select a an annotation bigger than another by selecting the part not behind the smaller one, it is still a problem for other situation as

• annotations with same dimensions
• annotation in a set of multiple annotations.

In "normal" mode, the workspace is not consider as active when we are in a specific project.

It should.

One of our main dependency is vuelayers.
When we develop this project, we based our features on the version 0.11.4 of vuelayers.

However, we face problems with infinite loop of feature selection with new versions (see #18 and #57 )

Even with the fix of the PR, we still have issues with rotation and translation.
With recent 0.11.x, it is impossible to select the source for the rotation (source "undefined" in https://github.com/cytomine/Cytomine-Web-UI/blob/master/src/vuelayers-suppl/rotate-interaction/interaction.vue#L61 )
With 0.11.7, it is possible to enable rotation but ...the undo doesn't work anymore -.-.

So as long as vue-layers is in version 0 (with potential breaking change with each release), I set the version to 0.11.4.
When there will be a version 1, we will need to test each frontend feature.

Expected :
Able to delete a vertex in the modification mode with a click on the vertex with the Alt key down.

Current :
I can't.

During a debugging, I can see that I can't have the two event simultaneously.

Hello,

I have encountered an issue with terms in cytomine.
They cannot be deleted. Neither via the web UI nor via the API.
When I try to delete them via the web UI, a message says, that it is successfully deleted, but after a refresh the term reappears and is also still fetchable via the api.
I am logged in as the default admin.

Situation :
When I hide some annotation informations in the Annotation details part of the CustomUI configuration, the annotation details panel in the viewer still have its size.

Expected : The panel is resized.