Opened 6 weeks ago

Last modified 10 days ago

#1271 new enhancement

HE glass images in the Histology wizard

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Reggie v4.28
Component: net.sf.basedb.reggie Keywords:
Cc:

Description (last modified by Nicklas Nordborg)

We have got scanned images of most of our HE glass slides. The images are very high resolution of the full glass in .ndpi format (NanoZoomer Digital Pathology Image). Basically it is a container with multiple TIF images in different resolutions. The largest TIF is about 60Kx60K pixels. A special program (NDP.view2) is required to view the images: https://www.hamamatsu.com/eu/en/product/type/U12388-01/index.html

We should be able to associate each image with a specific HE glass slide (using an any-to-any link) in BASE.

In the Histology scoring wizard, we should add a link to the image so that it is possible for the user to download and view the full image and use it for scoring.

If possible it could be nice to have the link to the full image also in the Case summary.

Change History (9)

comment:1 Changed 6 weeks ago by Nicklas Nordborg

Description: modified (diff)

comment:2 Changed 6 weeks ago by Nicklas Nordborg

In 6017:

References #1271: HE glass images in the Histology wizard

Added a link to the NDPI image for a HE slide. It is assumed to be linked with an any-to-any item named "NDPI Image".

comment:3 Changed 6 weeks ago by Nicklas Nordborg

In 6018:

References #1271: HE glass images in the Histology wizard

Added a link to the NDPI image for a HE slide to the case summary.

comment:4 Changed 6 weeks ago by Nicklas Nordborg

In 6020:

References #1271: HE glass images in the Histology wizard

Fixed an incorrect size specification for thumbnail images.

comment:5 Changed 11 days ago by Nicklas Nordborg

In 6049:

References #1271: HE glass images in the Histology wizard

Added thumbnail of the slide to the bioplate view page.

comment:6 Changed 11 days ago by Nicklas Nordborg

In 6050:

References #1271: HE glass images in the Histology wizard

Added thumbnail of the slides to the bioplates list page.

comment:7 Changed 11 days ago by Nicklas Nordborg

In 6051:

References #1271: HE glass images in the Histology wizard

Display a thumbnail of the full slide image in this wizard if it exists.

comment:8 Changed 11 days ago by Nicklas Nordborg

In 6052:

References #1271: HE glass images in the Histology wizard

Added the Thumbnails extension to the list of requirements for Reggie.

comment:9 Changed 10 days ago by Nicklas Nordborg

In 6055:

References #1271: HE glass images in the Histology wizard

Implemented functionality for displaying a preview of the label and the scanned area for a glass slide. The preview is displayed in the same space to the right that is used to display the preview for sample images. By clicking to the left/right on the full-slide thumbnail we will display a larger preview of either the label or scanned area.

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