ISA Project

Overview

Overview
Related items

Project Placeholder for ISA structure

Sponsor: This Trial Project is not associated with a Sponsor

SEEK ID: https://ldh-test.imise.uni-leipzig.de/projects/2

Public web page: Not specified

NFDI4Health PIs: No PIs for this Trial Project

Trial Project created: 23rd Sep 2022

Extended Metadata (Nfdi4Health MDS 3.3)

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Resource classification(*)

Type of the resource(*) : Not specified

Title(s)/name(s) of the Project

Title/name(*) : Not specified
Language of the title/name(*) : Not specified

Acronym(s) of the Project

Acronym(*) : Not specified
Language of the acronym(*) : Not specified

Description(s) of the Project

Description(*) : Not specified
Language of the description(*) : Not specified

Keyword(s) describing the Project

Keyword(*) : Not specified

Contributor(s) of the Project

Is it a personal or organisational contribution?(*) : Not specified
Details about the contributing organisation(s)/institution(s)/group(s)
Contributor type(*) : Not specified
Funding identifier(s) : Not specified
Name of the organisation/institution/group(*) : Not specified
Details about the contributing person(s)
Contributor type(*) : Not specified
Given name(*) : Not specified
Family name(s)(*) : Not specified
Digital identifier(s)
Identifier(*) : Not specified
Scheme(*) : Not specified
Email address : Not specified
Phone number : Not specified
Organisation(s) associated with the contributor
Name(*) : Not specified
Address : Not specified
Web page : Not specified
Digital identifier(s)
Identifier(*) : Not specified
Scheme(*) : Not specified

Alternative identifiers

Type of the registry(*) : Not specified
Identifier(*) : Not specified

Characteristics of the Project

Is it an interventional or non-interventional Project? : Not specified
Specification of the type of the Project
Interventional Project type : []
Non-interventional Project type : []
Primary health condition(s) or disease(s) considered in the Project
Primary health condition or disease name(*) : Not specified
Terminology/classification(*) : Not specified
Code of the health condition or disease : Not specified
Groups of diseases or conditions(*)
Which groups of diseases or conditions were the data collected on? : []
On which diseases or conditions were the data collected? : []
Collects mortality data? : Not specified
Administrative information about the Project
Status of the ethics committee approval : Not specified
Overall Project status : Not specified
Participants enrolled by invitation? : Not specified
Start date : Not specified
End date : Not specified
Mono- or multicentric? : []
Number of centers : Not specified
One or more data providers? : Not specified
Number of data providers : Not specified
Primary subject(*) : Not specified
Eligibility criteria for Project participants
Eligibility criteria: Minimum age
Minimum eligible age(*) : Not specified
Unit of age(*) : Not specified
Eligibility criteria: Maximum age
Maximum eligible age(*) : Not specified
Unit of age(*) : Not specified
Eligible gender : []
Inclusion criteria : Not specified
Exclusion criteria : Not specified
Population of the Project(*)
Coverage : Not specified
Country(ies) : []
Region(s) and/or city(ies) : Not specified
Interventions of the Project
Name of the intervention(*) : Not specified
Type of the intervention : Not specified
Additional information about the intervention : Not specified
Name(s) of the arm(s) associated with the given intervention : Not specified
Exposures of the Project
Name of the exposure : Not specified
Type of the exposure : Not specified
Additional information about the exposure : Not specified
Name(s) of the group(s) associated with the given exposure : Not specified
Outcome measures in the Project
Name of the outcome measure(*) : Not specified
Description of the outcome measure : Not specified
Type of the outcome measure : Not specified
Time point(s) of assessment : Not specified
Additional information about the Project : Not specified
Additional assessments/measurements in the Project : []
Data sharing strategy of the Project(*)
Is it planned to share the data?(*) : Not specified
Supporting documents available in addition to the data : []
When and for how long will the data be available? : Not specified
Criteria for data access : Not specified
Additional information about data sharing : Not specified
DataSHIELD/Opal infrastructure available? : Not specified
Link to data request application : Not specified
Web page with additional information about data sharing : Not specified
Record linkage possible? : Not specified
Non-interventional aspects of the Project
Temporal design : []
Target follow-up duration of the Project
Target follow-up duration(*) : Not specified
Unit of time(*) : Not specified
Number of follow-ups conducted : Not specified
Biosamples retained in a biorepository : []
Specific types of retained biosamples : Not specified
Interventional aspects of the Project
Numerical phase : Not specified
Masking of intervention(s) assignment
Masking implemented? : Not specified
Who is masked? : []
Additional information about masking : Not specified
Type of allocation of participants to an arm : Not specified
Off-label use of a drug product : Not specified

Related items

Advanced People list for this Trial Project with search and filtering

René Hänsel

Trial Projects:

Institutions: Default Institution, Institute for Medical Informatics, Statistics and Epidemiology (IMISE)

https://orcid.org/0000-0001-8344-0658

Frank Meineke

Trial Projects:

Institutions: Institute for Medical Informatics, Statistics and Epidemiology (IMISE)

Demo User

Trial Projects:

Institutions: Default Institution

Advanced Institutions list for this Trial Project with search and filtering

Default Institution

Country: United Kingdom

City: Not specified

Web page: Not specified

Institute for Medical Informatics, Statistics and Epidemiology (IMISE)

Country: Germany

City: Leipzig

Web page: https://www.imise.uni-leipzig.de/en/

Advanced Clinical Trials list for this Trial Project with search and filtering

test inv

ISA Project

No description specified

Submitter: René Hänsel

Sub-Studies: No Sub-Studies

Assays: No Assays

Snapshots: No snapshots

Created: 3rd Dec 2024 at 15:19

ISA Investigation

ISA Project

Placeholder Investigation for development purpose

Submitter: René Hänsel

Sub-Studies: Example Study 4, ISA Study, ISA Study as Substudy

Assays: ISA Ressource Exp. Assay, ISA Ressource Mod. Assay, Isa Sub Assy with Sample

Snapshots: Snapshot 1

Created: 23rd Sep 2022 at 11:38

Advanced Sub-Studies list for this Trial Project with search and filtering

ISA Study as Substudy

ISA Project

This a study as Substudy, where a investigation contians Study Metadata

Submitter: René Hänsel

Clinical Trial: ISA Investigation

Assays: Isa Sub Assy with Sample

Snapshots: No snapshots

Created: 13th Jan 2023 at 09:44

Example Study 4

ISA Project

No description specified

Submitter: Demo User

Clinical Trial: ISA Investigation

Assays: No Assays

Snapshots: No snapshots

Created: 19th Oct 2022 at 12:08

ISA Study

ISA Project

ISA Study as placeholder for development purpose

Submitter: René Hänsel

Clinical Trial: ISA Investigation

Assays: ISA Ressource Exp. Assay, ISA Ressource Mod. Assay

Snapshots: No snapshots

Created: 23rd Sep 2022 at 11:55

1 hidden item

Advanced Assays list for this Trial Project with search and filtering

ISA Ressource Exp. Assay

ISA Project

ISA Assay as placeholder for Development pupose

Submitter: René Hänsel

Assay type: Cell Growth Rate

Technology type: Microscopy

Clinical Trial: ISA Investigation

Sub-Study: ISA Study

SOPs: No SOPs

Data files: 1 hidden item

Snapshots: No snapshots

Created: 23rd Sep 2022 at 12:01, Last updated: 23rd May 2023 at 16:56

ISA Ressource Mod. Assay

ISA Project

ISA Mod. Assay as placeholder for development Purpose

Submitter: René Hänsel

Biological problem addressed: Metabolism

Clinical Trial: ISA Investigation

Sub-Study: ISA Study

SOPs: No SOPs

Data files: 1 hidden item

Snapshots: No snapshots

Created: 23rd Sep 2022 at 12:06, Last updated: 23rd May 2023 at 16:57

Isa Sub Assy with Sample

ISA Project

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Submitter: René Hänsel

Assay type: Experimental Assay Type

Technology type: Technology Type

Clinical Trial: ISA Investigation

Sub-Study: ISA Study as Substudy

SOPs: Test SOP

Data files: No Data files

Snapshots: No snapshots

Created: 17th Jan 2023 at 12:55, Last updated: 23rd May 2023 at 17:01

Advanced SOPs list for this Trial Project with search and filtering

Test SOP

ISA Project

No description specified

Creator: René Hänsel

Submitter: René Hänsel

Clinical Trials: ISA Investigation

Sub-Studies: ISA Study as Substudy

Resources: Isa Sub Assy with Sample

Created: 23rd May 2023 at 17:01

Advanced Publications list for this Trial Project with search and filtering

Fibrosis-4 (FIB-4) score at the primary care level: an analysis of over 160 000 blood samples.

ISA Project

Abstract

Not specified

Authors: D. Petroff, O. Batz, K. Jedrysiak, J. Kramer, T. Berg, J. Wiegand

Date Published: 5th Apr 2020

Publication Type: Journal

PubMed ID: 32245907

Citation: Gut. 2021 Jan;70(1):219-221. doi: 10.1136/gutjnl-2020-320995. Epub 2020 Apr 3.

Created: 3rd May 2023 at 12:16

Automated macrophage counting in DLBCL tissue samples: a ROF filter based approach.

ISA Project

Abstract (Expand)

BACKGROUND: For analysis of the tumor microenvironment in diffuse large B-cell lymphoma (DLBCL) tissue samples, it is desirable to obtain information about counts and distribution of different macrophage … subtypes. Until now, macrophage counts are mostly inferred from gene expression analysis of whole tissue sections, providing only indirect information. Direct analysis of immunohistochemically (IHC) fluorescence stained tissue samples is confronted with several difficulties, e.g. high variability of shape and size of target macrophages and strongly inhomogeneous intensity of staining. Consequently, application of commercial software is largely restricted to very rough analysis modes, and most macrophage counts are still obtained by manual counting in microarrays or high power fields, thus failing to represent the heterogeneity of tumor microenvironment adequately. METHODS: We describe a Rudin-Osher-Fatemi (ROF) filter based segmentation approach for whole tissue samples, combining floating intensity thresholding and rule-based feature detection. Method is validated against manual counts and compared with two commercial software kits (Tissue Studio 64, Definiens AG, and Halo, Indica Labs) and a straightforward machine-learning approach in a set of 50 test images. Further, the novel method and both commercial packages are applied to a set of 44 whole tissue sections. Outputs are compared with gene expression data available for the same tissue samples. Finally, the ROF based method is applied to 44 expert-specified tumor subregions for testing selection and subsampling strategies. RESULTS: Among all tested methods, the novel approach is best correlated with manual count (0.9297). Automated detection of evaluation subregions proved to be fully reliable. Comparison with gene expression data obtained for the same tissue samples reveals only moderate to low correlation levels. Subsampling within tumor subregions is possible with results almost identical to full sampling. Mean macrophage size in tumor subregions is 152.5+/-111.3 mum(2). CONCLUSIONS: ROF based approach is successfully applied to detection of IHC stained macrophages in DLBCL tissue samples. The method competes well with existing commercial software kits. In difference to them, it is fully automated, externally repeatable, independent on training data and completely documented. Comparison with gene expression data indicates that image morphometry constitutes an independent source of information about antibody-polarized macrophage occurence and distribution.

Authors: M. Wagner, R. Hansel, S. Reinke, J. Richter, M. Altenbuchinger, U. D. Braumann, R. Spang, M. Loffler, W. Klapper