Cytomine: Toward an Open and Collaborative Software Platform for Digital Pathology Bridged to Molecular Investigations

Summary: the article proposes new software platform for automating the processes of preprocessing and marking up datasets with the aim of further solving analytical problems such as image classification and processing textual and parametric information using neural network technologies. The software platform uses modern technologies and combines a large number of methods in the form of a modular platform, which can be supplemented as the tasks of analytical data processing become more complicated. The need to develop such a software platform is dictated primarily by the fact that, given the current level of data volume growth, the actual transition to deep data analytics remains unattainable without such software platforms, since confidentiality, access to information and the use of external data processing resources are required.

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Development of a Software Platform Based on Haptic Device for Surgery Simulators

International Congress on Human-Computer Interaction, Optimization and Robotic Applications Proceedings ◽

10.36287/setsci.4.5.004 ◽

2019 ◽

Author(s):

Nazmiye Ebru Duysak ◽

Emre Dandil ◽

Alpaslan Duysak

Keyword(s):

Haptic Device ◽

Software Platform

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A Digital Pathology Solution to Resolve the Tissue Floater Conundrum

Archives of Pathology & Laboratory Medicine ◽

10.5858/arpa.2020-0034-oa ◽

2020 ◽

Author(s):

Liron Pantanowitz ◽

Pamela Michelow ◽

Scott Hazelhurst ◽

Shivam Kalra ◽

Charles Choi ◽

...

Keyword(s):

Digital Pathology ◽

Primary Diagnosis ◽

Image Search ◽

Molecular Tests ◽

Tissue Identification ◽

Digital Database ◽

Glass Slides ◽

Search Tool ◽

Hematoxylin And Eosin ◽

Whole Slide Images

Context.— Pathologists may encounter extraneous pieces of tissue (tissue floaters) on glass slides because of specimen cross-contamination. Troubleshooting this problem, including performing molecular tests for tissue identification if available, is time consuming and often does not satisfactorily resolve the problem. Objective.— To demonstrate the feasibility of using an image search tool to resolve the tissue floater conundrum. Design.— A glass slide was produced containing 2 separate hematoxylin and eosin (H&E)-stained tissue floaters. This fabricated slide was digitized along with the 2 slides containing the original tumors used to create these floaters. These slides were then embedded into a dataset of 2325 whole slide images comprising a wide variety of H&E stained diagnostic entities. Digital slides were broken up into patches and the patch features converted into barcodes for indexing and easy retrieval. A deep learning-based image search tool was employed to extract features from patches via barcodes, hence enabling image matching to each tissue floater. Results.— There was a very high likelihood of finding a correct tumor match for the queried tissue floater when searching the digital database. Search results repeatedly yielded a correct match within the top 3 retrieved images. The retrieval accuracy improved when greater proportions of the floater were selected. The time to run a search was completed within several milliseconds. Conclusions.— Using an image search tool offers pathologists an additional method to rapidly resolve the tissue floater conundrum, especially for those laboratories that have transitioned to going fully digital for primary diagnosis.

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Integrated multi-modality image-guided navigation for neurosurgery: open-source software platform using state-of-the-art clinical hardware

International Journal of Computer Assisted Radiology and Surgery ◽

10.1007/s11548-021-02374-5 ◽

2021 ◽

Author(s):

Jonathan Shapey ◽

Thomas Dowrick ◽

Rémi Delaunay ◽

Eleanor C. Mackle ◽

Stephen Thompson ◽

...

Keyword(s):

Skull Base ◽

Open Source ◽

Open Source Software ◽

Skull Base Surgery ◽

Patient Specific ◽

Software Platform ◽

Image Guided ◽

Phantom Model ◽

Technical Requirements ◽

Navigated Ultrasound

Abstract Purpose Image-guided surgery (IGS) is an integral part of modern neuro-oncology surgery. Navigated ultrasound provides the surgeon with reconstructed views of ultrasound data, but no commercial system presently permits its integration with other essential non-imaging-based intraoperative monitoring modalities such as intraoperative neuromonitoring. Such a system would be particularly useful in skull base neurosurgery. Methods We established functional and technical requirements of an integrated multi-modality IGS system tailored for skull base surgery with the ability to incorporate: (1) preoperative MRI data and associated 3D volume reconstructions, (2) real-time intraoperative neurophysiological data and (3) live reconstructed 3D ultrasound. We created an open-source software platform to integrate with readily available commercial hardware. We tested the accuracy of the system’s ultrasound navigation and reconstruction using a polyvinyl alcohol phantom model and simulated the use of the complete navigation system in a clinical operating room using a patient-specific phantom model. Results Experimental validation of the system’s navigated ultrasound component demonstrated accuracy of $$<4.5\,\hbox {mm}$$ < 4.5 mm and a frame rate of 25 frames per second. Clinical simulation confirmed that system assembly was straightforward, could be achieved in a clinically acceptable time of $$<15\,\hbox {min}$$ < 15 min and performed with a clinically acceptable level of accuracy. Conclusion We present an integrated open-source research platform for multi-modality IGS. The present prototype system was tailored for neurosurgery and met all minimum design requirements focused on skull base surgery. Future work aims to optimise the system further by addressing the remaining target requirements.

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