mida-group / cytobrowser Goto Github PK

Reasonable error messages when no "image" give in the URL, or when the given image-file is missing.

Title says it all

For small images, the point marker symbol becomes too small.

Example
Run: ./examples/Zeiss-1-Stacked.sh (first download and unzip bftools from https://www.openmicroscopy.org/bio-formats/downloads/)

Show, below each button, how many existing annotations are made

See also: Selection @ http://picturae.github.io/openseadragonselection/

Make class labels and colors easily adjusted in a separate settings file.

The main Readme is nicely minimalistic, so perhaps a secondary file with a bit more details, including example with ndpisplit

Title says it all

Import from server option for the import, see #26

In shared session, add a checkbox (per person) to follow that person's view.

Delete option (trashbin) in the right-click menu

Right-click menu or something, to get a URL to send to collaborators
Depending on issue #1

Instead of buttons "Class 0" etc. use the following 7 classes

NILM, ASC-US, ASC-H, LSIL, HSIL, SCC, AdC

Taken from Zhang "DCCL: A Benchmark for Cervical Cytology Analysis"

"Based on The 2014 Bethesda System for Reporting Cervical Cytology
(2014 TBS) [12], the precancerous squamous intraepithelial lesions include four
types with an increasing level of severity: atypical squamous cells of undeter-
mined significance (ASC-US), low squamous intraepithelial lesion (LSIL), atypi-
cal squamous cell-cannot exclude HSIL (ASC-H) and high squamous intraepithe-
lial lesion (HSIL); while cancerous lesions include mainly two types: squamous
cell carcinoma (SCC) and adenocarcinoma (AdC)."
and "NILM (negative for intraepithelial lesion or malignancy)"

Current look:

Might be useful to know which level the cytopathologist was looking at.

Probably no need for drag-n-drop in the z-direction.

Fairly high prio
To enable us to start using the annotation with our Cytopathologist
Together with Issue #9

title says it all

Title says it all

Right-click or some field which pop's up for selected annotation objects where one can add free-text comments.
Extra good if it's noted who is commenting, see issue #29

Smarter loading than all layers at once, to speed things up a bit

Bug: Right click on annotation object, then ctrl-click to delete the object.
Behaviour: Object is deleted, but dialogue stays open.
Desired behaviour: Disable delete while dialogue is open.

Display only selected types/markers/by user/etc

Option to mark a region in the image.
Preferably with similar properties as markers, i.e., class, free-text info, etc.

1. Rectangular region
2. Polygonal region

The code should be refactored to have a clear, easily modifiable structure. In addition, unused code should be removed, code style should be consistent, and the code should be well-documented.

The current version of the Bootstrap CSS is 3.3.7, but the JS used is for version 4.0.0. The CSS should be updated to a more recent version so the two match, and the page should be updated to still work the same as it did with the old version.

Enable a linked viewport between collaborators
Presumably using some server side data
As responsive as possible (but not faster than that ;-) )

Use some URL token to connect views?

Title says it all.

Point and click interface to choosing which WholeSlide image to view.
Presumably based on the largest one-tile image in the dzi stack (the directory number can vary).

Enable use of URL with x,y,z position as encoded parameters

Would be nice to have some cookie with User information, to add as a stored field for annotations, comments, etc.
See also #28

the list update bugs

I do not see need for it, so simply disable instead of coding support.

See also: https://github.com/usnistgov/OpenSeadragonFiltering , https://github.com/picturae/OpenSeadragonImageFilters

When adding new markers to the overlay, the area in which click and drag events are triggered is often very large, and the clickable region around the visual marker seems to be different for different points. The points do not seem to always be centered in these regions either. The clickable region seems to move independent of the the points when dragging them, and they can even be dragged far enough to not include the point itself.

For phones and pads. (Will never be perfect)
dblclick for context menu?
region markers?

As of right now, collaborator cursors remain static when dragging markers. They should instead be shown to be responsible for moving the marker. Could have been done for issue #3, but saving it for after issue #22.

Marker, rectangle, polygon graphicon-buttons instead of words

With live interactive duplicate marker checks.

Some restricted directory tree where user can save annotations on the server
Try to keep security on mind, disallow change of extension, make sure to check filename for weird characters, pop-up question when overwriting an existing file (perhaps even versioned saves... if not too complicated).

Following a quick check that we're acknowledging who should be, and a double-check that the licence is correct

If first marking polygons, then double-click for second corner comes naturally, but gives undesired creation of new rectangle

Very low prio issue
With the full class names according to #9

Organize the directory structure a bit.
Suggested to rename app.js to cytobrowser.js
Put server side code into server/ directory

Comment field for the whole image

OpenSeadragon has the built-in ability to rotate the viewport with keyboard shortcuts, so it might be good to make this work well together with URL coordinates, viewport following, etc.

This makes a mess of drawing in some situations

To make it smoother to work with images+annotations

Enhancement on #3