3.11.0

3.11.0

Version 3.11 of quip/caMicroscope is at core about two new exciting additions to the platform! Thanks to @CGDogan for system-wide improvements and additions which have greatly expanded compatibility by including DICOM and Bioformats, and to @BryanGsep for work towards streamlined usability for machine learning tools.

Parallel to the release, caMicroscope has updated our website (https://camicroscope.github.io/), governance, the creator covenant, among other guides.

Distribution (https://github.com/camicroscope/Distro)

• Add configuration and route support for dicom server and related routes

Viewer (https://github.com/camicroscope/caMicroscope)

• Dicom and Bioformats Intergration (#647, #653, #655)
• Improved Machine Learning Toolkit (#658)

Backend (https://github.com/camicroscope/caracal)

• Faster dockerfile clone
• Add filesystem related handlers for DICOM
• Update node container base
• Update CI and tests
• Add a handler for finding a document using regex

Loader (https://github.com/camicroscope/SlideLoader)

• Add dicom and bioformats support
• Use the Image Decoders Base for Docker
• Refactor for relative path directories
• Refactor google drive related functionality

Tile Server (https://github.com/camicroscope/iipImage)

• Dicom and bioformats support and integration
• Use the Image Decoders Base for Docker

Dicom Server (https://github.com/camicroscope/dicomsrv)

• New service for dicom integration

3.10.1

Viewer

• Bugfix for spyglass tool with token slide auth

3.10.0

Distro

• Support for Slide Token Check Option Distro/196
• Update Pathdb to 2.0.0 and Pathdb Image Loader to 3.0.0
• Github CI Distro/197

Viewer

• Result Export Page caMicroscope/566
• Slide Token injection caMicroscope/567

Backend

• Add Pathdb Token Slide Auth Handler Caracal/139
• Support using files as immediate backups for data Caracal/102
• Switch (back) to alpine container base

SlideLoader

• Simplify/refactor thumbnail script

PathDB

• Updated to PHP 8.1 and Drupal 9

3.9.9

Distro

• Upgrade mongo to 4.2-bionic

Viewer

Fix and enhance Human Readable URL support

3.9.8

Distro

• add youtube-nocookie to csp config for embed video
• add openshift config

Viewer

• Add Segmentation -> Annotation Functionality #542
• Margin and Table UI Fixes #549 #551
• Add Pathdb Quad Lookup
• Add Docs link to landing
• retry slides one time if they have an error

Backend

• disable tfjs for production reasons

Slide Loader

• Support more metadata extraction, optionally

3.9.7

Pathdb

• Update to 1.7.0

Backend

• Slide param for mark/multi bugfix

3.9.6

Distro

• update marks with labels
• include a sample segmentation
• dependency upgrade #171

Viewer

• Some integration with the "Smartpen" concept #526, #532
• Preset label bugfix

Backend

• Route Validation #122, #118
• Fixes for Preset Label

Segmentation Loader

• Assign colors to different classes of nuclei.

3.9.4

Heatmap Utility - https://github.com/SBU-BMI/uploadHeatmaps

• EOL Bugfix

3.9.3

• Bugfix for additional links url
• Additional links can launch with slide id

3.9.2

Distro

• New Pathdb Version
• Add Configurable CSP headers
• Add Configurable Links
• Readme improvements and fixes

Viewer

• Github action for ci testing #502
• Validate Emails on signup #501
• Image Enhancements #500
• Configurable Toolbar Links #511
• Documentation Improvements #506

SlideLoader

• Omniload Pathdb Bugfix

Backend

• Add configurable CSP headers #83
• package.json fix #72
• Support .env for environment variables #75
• Github Workflow for CI