cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.3535/9w8-qsm-xhn
title: Catoptria falsella [Denis & Schiffermüller], 1775

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/myp-rd9-rzt
title: Orthosia (Monima) populeti Fabricius, 1781

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ngg-pl7-wh4
title: Agriphila tristellus [Denis & Schiffermüller], 1775

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/tqw-5fd-km1
title: Orthosia (Monima) populeti Fabricius, 1781

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/542-20d-f6t
title: Dypterygia scabriuscula (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/zyw-mbv-wh8
title: Dypterygia scabriuscula (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/968-7zn-2wk
title: Exaeretia ciniflonella Zeller, 1846

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/szd-9cp-6en
title: Plusia festucae (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/3xz-d3e-bsr
title: Orgyia (Telochurus) recens (Hübner, 1819)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ry1-kr0-0yd
title: Zophodia convolutella Hübner, 1796

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/tmg-kqs-sxj
title: Zophodia convolutella Hübner, 1796

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/w38-fqt-a3r
title: Plusia putnami Grote, 1873

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/wjw-qtk-j0c
title: Exaeretia allisella Stainton, 1849

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/z0k-646-t67
title: Phengaris Doherty, 1891

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/klx-h6z-l31
title: Tetheella fluctuosa (Hübner, 1803)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/z82-3bs-rnw
title: Agriphila selasella Hübner

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0lx-9qz-3q6
title: Dichonia (Griposia) Tams, 1939

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/65g-ckq-cdx
title: Tetheella fluctuosa (Hübner, 1803)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/xet-h6e-ewf
title: Caradrina (Platyperigea) montana Bremer, 1864

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/7rz-jgl-8jk
title: Agriphila inquinatella [Denis & Schiffermüller], 1775

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/e3f-47b-f5a
title: Exaeretia allisella Stainton, 1849

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/pkt-bj4-89p
title: Orthosia (Monima) populeti Fabricius, 1781

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/we1-0zx-wkt
title: Agriphila tristellus [Denis & Schiffermüller], 1775

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/yyg-594-sj6
title: Plusia putnami Grote, 1873

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/s29-b6r-0lh
title: Orthosia (Monima) populeti Fabricius, 1781

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/8t6-3zd-b5j
title: Agriphila selasella Hübner

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sb8-jv1-l7m
title: Phengaris Doherty, 1891

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/2wq-cld-s21
title: Diachrysia chrysitis (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/5y3-hj1-crh
title: Agriphila inquinatella [Denis & Schiffermüller], 1775

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/twm-lsv-1kh
title: Phengaris Doherty, 1891

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/fa8-114-2dc
title: Autographa Hübner, 1821

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/nt5-ej1-vf1
title: Catoptria falsella [Denis & Schiffermüller], 1775

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/s7b-kj7-5sw
title: Lasionycta Aurivillius, 1892

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/w1a-nf6-p50
title: Athetis (Hydrillula) Tams, 1938

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/wjs-xjf-fsf
title: Agriphila inquinatella [Denis & Schiffermüller], 1775

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/4pw-5qe-cbc
title: Autographa Hübner, 1821

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/psv-d4s-vjh
title: Dichonia (Griposia) Tams, 1939

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/xbt-p65-t2j
title: Sciota hostilis Stephens, 1834

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/49w-1a3-kdn
title: Plodia interpunctella (Hübner, 1813)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/n1x-8jp-a02
title: Phengaris Doherty, 1891

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/4by-7rg-ak3
title: Conistra (Conistra) vaccinii (Linnaeus, 1761)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/4pr-fmr-1qv
title: Agriphila inquinatella [Denis & Schiffermüller], 1775

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/48c-lde-rbf
title: Athetis (Hydrillula) Tams, 1938

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/vx8-wg7-br3
title: Opigena polygona [Denis & Schiffermüller], 1775

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ptp-vnc-m1e
title: Conistra (Conistra) vaccinii (Linnaeus, 1761)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/mgx-yrw-3ve
title: Dichonia (Griposia) Tams, 1939

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/qhz-ece-h7y
title: Exaeretia allisella Stainton, 1849

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/e5h-ewt-s8z
title: Mythimna (Mythimna) impura Hübner, 1808

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/xjr-9c0-6t0
title: Dichonia (Griposia) Tams, 1939

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/g15-lqn-ksp
title: Mythimna (Mythimna) impura Hübner, 1808

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sp6-kdn-t09
title: Exaeretia allisella Stainton, 1849

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.6084/m9.figshare.30795206.v2
title: düsük hapı fiyatı 0546 268 58 32 düsük ilacı fiyatı

description: düsük hapı fiyatı 0546 268 58 32 düsük ilacı fiyatı düsük hapı fiyatı 0546 268 58 32 düsük ilacı fiyatı düsük hapı fiyatı 0546 268 58 32 düsük ilacı fiyatı düsük hapı fiyatı 0546 268 58 32 düsük ilacı fiyatı düsük hapı fiyatı 0546 268 58 32 düsük ilacı fiyatı düsük hapı fiyatı 0546 268 58 32 düsük ilacı fiyatı düsük hapı fiyatı 0546 268 58 32 düsük ilacı fiyatı düsük hapı fiyatı 0546 268 58 32 düsük ilacı fiyatı düsük hapı fiyatı 0546 268 58 32 düsük ilacı fiyatı düsük hapı fiyatı 0546 268 58 32 düsük ilacı fiyatı düsük hapı fiyatı 0546 268 58 32 düsük ilacı fiyatı düsük hapı fiyatı 0546 268 58 32 düsük ilacı fiyatı düsük hapı fiyatı 0546 268 58 32 düsük ilacı fiyatı düsük hapı fiyatı 0546 268 58 32 düsük ilacı fiyatı düsük hapı fiyatı 0546 268 58 32 düsük ilacı fiyatı düsük hapı fiyatı 0546 268 58 32 düsük ilacı fiyatı düsük hapı fiyatı 0546 268 58 32 düsük ilacı fiyatı düsük hapı fiyatı 0546 268 58 32 düsük ilacı fiyatı düsük hapı fiyatı 0546 268 58 32 düsük ilacı fiyatı düsük hapı fiyatı 0546 268 58 32 düsük ilacı fiyatı düsük hapı fiyatı 0546 268 58 32 düsük ilacı fiyatı düsük hapı fiyatı 0546 268 58 32 düsük ilacı fiyatı düsük hapı fiyatı 0546 268 58 32 düsük ilacı fiyatı düsük hapı fiyatı 0546 268 58 32 düsük ilacı fiyatı düsük hapı fiyatı 0546 268 58 32 düsük ilacı fiyatı düsük hapı fiyatı 0546 268 58 32 düsük ilacı fiyatı düsük hapı fiyatı 0546 268 58 32 düsük ilacı fiyatı düsük hapı fiyatı 0546 268 58 32 düsük ilacı fiyatı düsük hapı fiyatı 0546 268 58 32 düsük ilacı fiyatı düsük hapı fiyatı 0546 268 58 32 düsük ilacı fiyatı düsük hapı fiyatı 0546 268 58 32 düsük ilacı fiyatı düsük hapı fiyatı 0546 268 58 32 düsük ilacı fiyatı düsük hapı fiyatı 0546 268 58 32 düsük ilacı fiyatı
DOI: 10.3535/3vj-t8k-ncg
title: Athetis (Hydrillula) Tams, 1938

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/6f3-0rr-7t4
title: Catoptria falsella [Denis & Schiffermüller], 1775

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/bhb-63s-3h4
title: Orthosia (Monima) populeti Fabricius, 1781

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/jv8-nfc-ky2
title: Athetis (Hydrillula) Tams, 1938

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/njs-ymg-2mg
title: Cucullia umbratica (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/2bk-lzb-baj
title: Agrochola (Anchoscelis) Guenée, 1839

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/9l5-hk5-5nm
title: Eugnorisma (Metagnorisma) depuncta Linnaeus, 1761

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/b26-e2b-rrv
title: Pheosia gnoma (Fabricius, 1776)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/c5g-yzc-gjb
title: Agrochola (Anchoscelis) Guenée, 1839

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/452-djj-php
title: Fabriciana adippe ([Denis & Schiffermüller], 1775)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/rea-5ym-k6y
title: Fabriciana adippe ([Denis & Schiffermüller], 1775)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/9vp-efk-wlk
title: Zophodia convolutella Hübner, 1796

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/kkk-w4h-4xa
title: Dasypolia (Dasypolia) templi Thunberg, 1792

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/xkc-6ea-ltj
title: Cucullia umbratica (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/zag-qsy-3wn
title: Drepana falcataria (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.17026/ar/tmacbi
title: PAN-00167252 - solid iron chisel

description: &lt;p&gt;This find is registered at Portable Antiquities of the Netherlands with number PAN-00167252&lt;/p&gt;
description: Modified: 2025-06-30T12:08:00+02:00
DOI: 10.3535/8dq-y2e-rsd
title: Eugnorisma (Metagnorisma) depuncta Linnaeus, 1761

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ywg-5nq-33d
title: Amphipoea fucosa Freyer, 1830

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/8ga-0hx-bsx
title: Agrochola (Anchoscelis) Guenée, 1839

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/lwp-8lz-66c
title: Lithophane (Lithophane) consocia Borkhausen, 1792

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/rej-led-s8e
title: Drepana falcataria (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/780-9b8-dw2
title: Colobochyla salicalis ([Denis & Schiffermüller], 1775)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/qln-e2s-zt5
title: Actebia (Actebia) praecox Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/gqy-dqa-twv
title: Zophodia convolutella Hübner, 1796

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/qvg-rrt-8js
title: Hypochalcia ahenella [Denis & Schiffermüller], 1775

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/fwt-nm8-bbw
title: Diachrysia chrysitis (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/s1c-l3t-rqt
title: Drepana falcataria (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/5jf-62r-3w8
title: Xestia (Pachnobia) alpicola Zetterstedt, 1840

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/qj4-ncx-tjy
title: Erebia lappona Thunberg, 1791

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/qnt-m8a-j13
title: Drepana falcataria (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/8z6-gy6-d8x
title: Fabriciana adippe ([Denis & Schiffermüller], 1775)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/kme-lq2-1nc
title: Lithophane (Lithophane) consocia Borkhausen, 1792

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/aay-wt1-hqf
title: Mythimna (Mythimna) impura Hübner, 1808

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/gd7-x4x-ejb
title: Pyla fusca Haworth, 1811

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/w7v-pbh-2sp
title: Colobochyla salicalis ([Denis & Schiffermüller], 1775)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/4me-jbm-7jl
title: Rhizedra lutosa Hübner, 1803

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/wnb-wxk-4xe
title: Papilio machaon Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/867-gx7-h2m
title: Actebia (Actebia) fennica Tauscher, 1806

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/asw-g4g-25b
title: Acronicta (Subacronicta) megacephala ([Denis & Schiffermüller], 1775)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/h9r-ktq-8gn
title: Papilio machaon Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/r6h-0w3-gpv
title: Rhizedra lutosa Hübner, 1803

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/575-97v-2p1
title: Rhizedra lutosa Hübner, 1803

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/egs-qlx-3d7
title: Lasionycta Aurivillius, 1892

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/d69-mr8-fr3
title: Fabriciana adippe ([Denis & Schiffermüller], 1775)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/s9x-1fq-gse
title: Xestia (Pachnobia) alpicola Zetterstedt, 1840

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.5281/zenodo.17407977
title: Reproducible Research Platform Player Bundle for Deep learning, ML and LLM Player Bundle

description: RRP Deep learning, ML and LLM

Reproducible Research Platform (RRP) project for deep learning or machine learning applications.

Overview

This RRP project repository demonstrates how to train a deep learning model for cell segmentation of microscopy data mounted from the research data management system (RDMS) openBIS ELN-LIMS. Microscopy data is managed in the RDMS and annotated with respective metadata. Using their permID the data is directly available in the RRP project for analysis and can be integrated in reproducible workflows.

The main outcome of this example is:



Training a DL model for image segmentation.

Visualization of the model predictions.

Example of LLM assisting analysis.


Features



Integration with RRP and openBIS ELN--LIMS: mounts data (microscopy) from the research data management system openBIS in RRP for direct use.

Reproducible workflow: Notebooks document interactions.

Visualization: Generates visualizations of the model predictions.


Installation

 

Prerequisites



Local Docker installation.


Steps



Download and extract the .zip file

Run the play script for your operating system



Linux / macOS: play

Windows: play.bat or play.ps1




Usage

In RRP open and run the Jupyter notebook run_model_training.ipynb and after the training the run_LLM_assistance.ipynb

Workflow Overview



Training: Train a DL model for image segmentation

Visualization: Visualize model predictions

LLM assistance: Example how LLM can assist analysis.


Directory Structure



├── .binder/                               # Environment specifications, Python version, packages (qute) etc.
├── .rrp/                                  # Specification of openBIS server and required data from RDMS openBIS ELN-LIMS (Microscopy data)
├── cell_segmentation_demo_unet.py         # Python script for segmentation model training 
├── cell_segmentation_demo_unet_config.ini # Config file for segmentation model training
├── prepare_data.sh                        # Prepares image data for deep learning 
├── LICENSE                                # License
├── README.md                              # This file
├── run_LLM_assistance.ipynb               # Notebook demonstrating LLM help for image analysis
└── run_model_training.ipynb               # Notebook to train the DL model


Contributing

We welcome contributions to improve this repository! Please follow these steps:



Fork the repository.

Create a new branch for your feature or bug fix.

Submit a pull request with a clear description of your changes.


Authors and acknowledgment



Andreas P. Cuny, ETH Zurich initial implementation


License

This project is licensed under the Apache 2.0 License. See LICENSE file for details.

Copyright © 2020-2025 ETH Zurich, Andreas P. Cuny, D-BSSE, CSB Group
DOI: 10.5281/zenodo.17407978
title: Reproducible Research Platform Player Bundle for Deep learning, ML and LLM Player Bundle

description: RRP Deep learning, ML and LLM

Reproducible Research Platform (RRP) project for deep learning or machine learning applications.

Overview

This RRP project repository demonstrates how to train a deep learning model for cell segmentation of microscopy data mounted from the research data management system (RDMS) openBIS ELN-LIMS. Microscopy data is managed in the RDMS and annotated with respective metadata. Using their permID the data is directly available in the RRP project for analysis and can be integrated in reproducible workflows.

The main outcome of this example is:



Training a DL model for image segmentation.

Visualization of the model predictions.

Example of LLM assisting analysis.


Features



Integration with RRP and openBIS ELN--LIMS: mounts data (microscopy) from the research data management system openBIS in RRP for direct use.

Reproducible workflow: Notebooks document interactions.

Visualization: Generates visualizations of the model predictions.


Installation

 

Prerequisites



Local Docker installation.


Steps



Download and extract the .zip file

Run the play script for your operating system



Linux / macOS: play

Windows: play.bat or play.ps1




Usage

In RRP open and run the Jupyter notebook run_model_training.ipynb and after the training the run_LLM_assistance.ipynb

Workflow Overview



Training: Train a DL model for image segmentation

Visualization: Visualize model predictions

LLM assistance: Example how LLM can assist analysis.


Directory Structure



├── .binder/                               # Environment specifications, Python version, packages (qute) etc.
├── .rrp/                                  # Specification of openBIS server and required data from RDMS openBIS ELN-LIMS (Microscopy data)
├── cell_segmentation_demo_unet.py         # Python script for segmentation model training 
├── cell_segmentation_demo_unet_config.ini # Config file for segmentation model training
├── prepare_data.sh                        # Prepares image data for deep learning 
├── LICENSE                                # License
├── README.md                              # This file
├── run_LLM_assistance.ipynb               # Notebook demonstrating LLM help for image analysis
└── run_model_training.ipynb               # Notebook to train the DL model


Contributing

We welcome contributions to improve this repository! Please follow these steps:



Fork the repository.

Create a new branch for your feature or bug fix.

Submit a pull request with a clear description of your changes.


Authors and acknowledgment



Andreas P. Cuny, ETH Zurich initial implementation


License

This project is licensed under the Apache 2.0 License. See LICENSE file for details.

Copyright © 2020-2025 ETH Zurich, Andreas P. Cuny, D-BSSE, CSB Group