Zsolt SZEGEDI MD senior development manager

Distributor Training, 2017, Budapest, Hungary Vendor-specific digital slide types

• 3DHISTECH • Olympus • MRXS • VSI • DICOM • Philips • Leica-Aperio • TIFF • SVS • Roche-Ventana • SCN • BIF • TIFF • TIF • DICOM • Sakura • Hamamatsu • SVSLIDE • VMS • Trestle • VMU • TIFF • NDPI • Zeiss-Mirax • DICOM • MRX

Distributor Training, 2017, Budapest, Hungary Content and structure of a digital slide Thumbnail image

Intermediate image

Baseline image

• Hierarchical part • type • Zoom-level (pyramid model) • Raw (e.g. Hamamatsu) • Filter-level (fluorescent slides) • JPEG-XR, PNG (e.g. 3DHISTECH) • Z-stack (3rd dimension) • JPEG2000 (e.g. Leica) • Non-hierarchical part • Lossless JPEG (e.g. DICOM) • Thumbnail • LZW-encoded • Label area (barcode) • Content description format • Annotations • Own standard (e.g. DICOM) • Measurements • XML (e.g. Philips, 3DHISTECH) • Security checksum • Registered TIFF-tags (e.g. Hamamatsu) • Stitching map • Not documented (e.g. 3dHISTECH)

Distributor Training, 2017, Budapest, Hungary Desktop SlideConverter

Distributor Training, 2017, Budapest, Hungary Licensing of the slide formats

INTERNAL: EXTERNAL: Allowed formats are stored by a Dongle key User have to register individually Using SDKs from 3rd party vendors Only for DICOM format

FREE: No extra license required - MRXS (3DHISTECH default format) - Images (JPG, PNG, BMP, TIFF, bigTIFF)

Distributor Training, 2017, Budapest, Hungary SlideConverter file formats MRXS: 3DHISTECH R-TIFF: Roche slide SVS: Leica-Aperio T-TIFF: Tiled TIFF (FL-channels and Z-stacks) NDP: Hamamatsu B-TIFF: simple or big (> 4096x4096) TIFF DICOM: DICOM WG26 IMG: JPEG, PNG, BMP, TIFF (small)

Source MRXS SVS NDP R-TIFF T-TIFF B-TIFF IMG DICOM Destination MRXS - L L L F F L SVS L - L* L* L* L* L* NDP - R-TIFF L L* L* - L* L* L* T-TIFF F L* L* L* - F* F* L* B-TIFF - IMG - DICOM L L* L* L* L* L* - F : free L : licensed - : identical * : multiple steps

Distributor Training, 2017, Budapest, Hungary Logging the conversion process

Turning ON/OFF logging Folder of the log files

File name (containing the date+time): e.g. converter_log_20160317143005.xml

Content of the log XML: • Input slide name and format • Output slide name and fomat • Parameters of the conversion • Start time • Status • Error messages • Finish time • Steps and times of the conversion

Default parameters by slide types: MRXS, SVS, NDPI, Roche-TIFF, TIFF, image (JPG, PNG, BMP)

Distributor Training, 2017, Budapest, Hungary SlideConverter GUI

Distributor Training, 2017, Budapest, Hungary SlideConverter sources

Local file CaseCenter CaseViewer

Refresh folder-tree: Connecting to a server Automatic mode or change to another (when started from CV) Non-recursive or account: recursive search: Open folder: Login:

Select folder:

Distributor Training, 2017, Budapest, Hungary Conversion types: writing MRXS

Open properties: Set properties:

SVS to MRXS: read Leica-Aperio slide Rotate slide: correct the orientation

Image to MRXS: read plain TIFF, JPEG, PNG or BMP image Change resolution: width x height

MRXS to MRXS: for shrinking overlapped slides Annotations only: excludes image info which are not under an annotation Allow reconverting: excludes non-necessary (like morphometry) meta-data

MDP to MRXS: read Hamamatsu slide Color correction: balancing brightness, contrast and gamma values Rotate slide: correct the orientation

Distributor Training, 2017, Budapest, Hungary Conversion types: reading MRXS MRXS to DICOM: writing whole slide image (WSI) DICOM Frame number Optical path / frame size, depth and X-Y offset accuracy Tile pool size UTC time Basic offset table Shared plane position Shared optical reference

MRXS to R-TIFF: writing Roche-TIFF Compression type: uncompressed or JPEG (80)

MRXS to T-TIFF: writing multiple (tiled) TIFF files Zero-based index: file numbering from 0 or by focus distance Type: auto, simple or big-TIFF Compression: JPG (8 bit), lossless (8/16 bit), uncompressed (8/16 bit)

MRXS to SVS: writing Leica-Aperio slide Compression type: uncompressed or JPEG (80)

Distributor Training, 2017, Budapest, Hungary SlideConverter queue

Delete selected Start / Stop conversion Delete all

Multi-thread setting Delete finished

Possible statuses: Queued In progress Finished

Error Stopping Stopped

Distributor Training, 2017, Budapest, Hungary Command-line conversion parameters --source-format --destination-format --step-width --step-height --use-threads Special parameters for DICOM: --number-of-threads --dicom-parameters --thread-priority max-frame-number --memory basic-offset-table --archive utc-bias --archive-annotations pixel-size-accuracy --dearchive xy-accuracy --rotate depth-accuracy --resolution-x plane-pos-shared --resolution-y optical-ref-shared ---type tile-pool-size --destination-brightness-hamamatsu merged-channels --destination-contrast-hamamatsu --destination-gamma-hamamatsu Keyboard effects: --allow-nols --delete-input + / - change Nr of threads --tiled-tiff-zero-based-index ↑ / ↓ change thread priority --tiled-tiff-compression-mode Esc Finish conversion

Distributor Training, 2017, Budapest, Hungary New features of te SlideConverter ver.2.1 • Access from the CaseCenter: import/export all known formats • Automatic command-line (batch) process by the scanner software • Export annotated areas into new slides from the CaseViewer • Archiving: leave all images associated to annotations, erase otherwise ver.2.2 • Automatic de-overlapping conversion on the scanner PC • Selectable zoom level (actually the default is the largest) • Running speed optimalisation (skip unnecessary re-coding or re-tiling)

Distributor Training, 2017, Budapest, Hungary DICOM-related development

Distributor Training, 2017, Budapest, Hungary Implementation state of the DICOM standard

• SlideAC API can read DICOM files: • CaseViewer can open local DICOM slides • SlideConverter can use any WSI DICOM source (at least zoom level 10)

• Slide size limitation: • Actually small (1-3 GB) DICOM slides can be handled • Switch off the „Basic Offset Table” allows larger size • No size limitation during slide conversion (tested up to 100GB)

• Speed: • Actually the opening speed is slow • The order of the tiles is sequential in DICOM

• Support of pseudo-colors: • It is used in case of fluorescent images (multiple color channels) • It is solved during MRXS to DICOM and DICOM to MRXS conversion

• Image encoding: • DICOM standard does not support JPEG-XR (which we prefer in MRXS) • Conversion to JPEG-2000 is slow but CaseViewer can display FL-DICOM

Distributor Training, 2017, Budapest, Hungary Next steps in the DICOM-related development

• Slide size limitation: • No limititation in CaseViewer after rewriting to 64bit architecture

• Speed: • Extension to a non-conventional tile mapping • Usage of the frame level retrieve technology

• Patient data: • DICOMDIR production containing patient- and case-data • Communication between the converter and the HIS/LIS • Restructuring patient-case-specimen-block-slide hierarchy for TMA

• DICOM logistics: • Sending DICOM to a PACS server or other DICOM nodes • Communication with WorkList servers (or create our own)

• DICOM-related projects: • 50-lab network, Sectra Inc (Sweden) • Scanner + SlideConverter + PACS hospital network, Baku (Azerbaijan)

Distributor Training, 2017, Budapest, Hungary 3DHISTECH’s DICOM on Sectra’s PACS server

www.sectra.com/vendor_neutral_pathology_3dhistech

Distributor Training, 2017, Budapest, Hungary The End