README file Data Set Title: Data relative to histology analyses from the publication "Perfusion-based ex vivo culture of frozen ovarian cancer tissues with preserved tumor microenvironment" Data Set Author: Monica De Luise (University of Bologna, Department of Medical and Surgical Sciences), ORCID 0000-0002-3486-3985; Data Set Contributor: Ivana Kurelac (University of Bologna, Department of Medical and Surgical Sciences), ORCID 0000-0002-8364-9985; Data Set Contact Persons: Giuseppe Gasparre (University of Bologna, Department of Medical and Surgical Sciences), ORCID 0000-0003-1229-9006, e-mail giuseppe.gasparre3@unibo.it; Manuele Giuseppe Muraro (University of Basel and University Hospital of Basel, Dept. of Biomedicine, Tissue Engineering), ORCID 0000-0002-4590-1916, e-mail manuele.muraro@unibas.ch; Data Set License: this data set is distributed under a Creative Commons Attribution 4.0 International (CC BY 4.0) license, https://creativecommons.org/licenses/by/4.0/ Publication Year: 2025 Project Info: the research leading to these results received funding from _project AMICO (Assessing the Efficacy of Mitochondrial Complex I Targeting in Combined Therapies for Ovarian Cancer), funded by Associazione Italiana Ricerca sul Cancro (AIRC), grant number IG 2019 - ID 22921 _project The underestimated role of the human omentum in metastatic spread, funded by the Swiss National Science Foundation grant number 171037, https://data.snf.ch/grants/grant/171037 _project MOnARCHY (Dissecting the Metabolic signature of epithelial OvARian cancer: a challenge to overcome CHemotherapY resistance), funded by Associazione Italiana Ricerca sul Cancro (AIRC) grant number IG 2020 - ID 24494 _project EMOTICON (Exploiting advanced MOdels to Target glucose deprivation resistance during anti-angiogenIC therapy in OvarianN cancer), funded by the Italian Ministry of University and Research, PRIN 2022 funding programme, grant agreement 202272LY8W _M.D.L. research contract co-funded by the European Union - PON Research and Innovation 2014-2020, pursuant to art. 24, paragraph 3, letter a), of Law no. 240 of December 30, 2010, as amended, and Ministerial Decree no. 1062 of August 10, 2021. Data set Contents The data set consists of: _15 compressed folders with 348 images in .ndpi, .ome.tif /.ome.tiff, or .tif, formats: De_Luise_HE_part01.zip De_Luise_HE_part02.zip De_Luise_HE_part03.zip De_Luise_HE_part04.zip De_Luise_HE_part05.zip De_Luise_HE_part06.zip De_Luise_aSMA_CD31_part01.zip De_Luise_aSMA_CD31_part02.zip De_Luise_Ki67.zip De_Luise_PAX8_part01.zip De_Luise_PAX8_part02.zip De_Luise_PAX8_part03.zip De_Luise_PAX8_part04.zip De_Luise_CD45.zip De_Luise_D2-40.zip _5 scripts and the relative classifiers in .txt format Neoplastic_cells_classification_from_HE.txt aSMA_cells_classification_and_count.txt Ki67_ECAD.txt PAX8_nuclei_area_measurements.txt CD45_cells_classification_and_count.txt _1 README file in .txt format De_Luise_histology-analyses_README.txt Data set Documentation Abstract Ovarian cancer (OC) poses significant treatment challenges due to late-stage diagnosis and a complex tumor microenvironment contributing to therapy resistance. We here deposited the data which allowed optimization of a U-CUP perfusion-based bioreactor method to culture patient-derived primary and metastatic OC specimens, demonstrating that perfusion better preserves cancer cell viability and proliferation, both when fresh and slow-frozen tissues were used. Specifically, histology analyses include: hematoxylin/eosin staining, PAX8 immunohistochemistry, Ki67/ECad immunofluorescence, αSMA/CD31 immunofluorescence, CD45 immunohistochemistry, D2-40 immunohistochemistry. Content of the files _Folders De_Luise_HE_part01-06.zip contain 75 images from HE stained tissues of 10 patients: OC1, OC2, OC3 (in De_Luise_HE_part01.zip), OC4 and OC5 (in De_Luise_HE_part02.zip), OC6 and OC7 (in De_Luise_HE_part03.zip), OC8, OC11, OC13 (in De_Luise_HE_part04.zip), OC14, OC15 (in De_Luise_HE_part05.zip) and OC16, OC17 (in De_Luise_HE_part06.zip). Inside each .zip archive, each folder contains the images of a specific patient. Patient OC5 images are further subdivided into two subfolders: OC-5_DM (DM-diaphragmatic metastasis) and OC-5_OV (OV-ovary). The same for patient OC11 images: they are further split into subfolders OC11_OM (OM-omental metastasis) and OC11_OV (OV-ovary). The images have been analyzed at various conditions, as indicated in the name of each image file (see the following File naming rules section). _Folders De_Luise_aSMA_CD31_part01-02.zip contain 20 immunofluorescence images of αSMA/CD31 marked tissues of 11 patients: OC1, OC2, OC3 (in De_Luise_aSMA_CD31_part01.zip), and OC4, OC5, OC7, OC11, OC14, OC15, OC16, OC17 (in De_Luise_aSMA_CD31_part02.zip). The file names of patient OC5 images indicate two tumor sites: OC5_DM (DM – diaphragmatic metastasis) and OC5_OV (OV – ovary). For patient OC11, the sample analyzed is specified as OC11_OM (omental metastasis). These tissues have been analyzed at various conditions as indicated in the name of each image file (see the following File naming rules section). _Folder De_Luise_Ki67.zip contains 168 immunofluorescence images of regions of interest (ROI) from Ki67/ECad marked tissues of 11 patients: OC1, OC2, OC3, OC4, OC5, OC7, OC11, OC14, OC15, OC16, OC17. The images related to each patient are included in a folder named with the patient ID. Patient OC5 images are subdivided into two folders: OC5_DM (DM-diaphragmatic metastasis) and OC5_OV (OV-ovary). The images of patiet OC11 are focused on the omental metastasis (OM, folder OC11_OM). The images have been analyzed at various conditions as indicated in the name of each image file (see the following File naming rules section). _Folders De_Luise_PAX8_part01-04.zip contain 56 immunohistochemistry images from PAX8 marked tissues of 11 patients: OC1 (in De_Luise_PAX8_part01.zip), OC2, OC3, OC4 (in De_Luise_PAX8_part02.zip), OC5, OC7, OC11, and OC14 (in De_Luise_PAX8_part03.zip), and OC15, OC16, and OC17 (in De_Luise_PAX8_part04.zip). The file names of patient OC5 images indicate two tumor sites: OC5_DM (DM-diaphragmatic metastasis) and OC5_OV (OV-ovary). These tissues have been analyzed at various conditions as indicated in the name of each image file (see the following File naming rules section). _Folder De_Luise_CD45.zip contains 21 immunohistochemistry images from CD45 marked tissues of 11 patients: OC1, OC2, OC3, OC4, OC5, OC7, OC11, OC14, OC15, OC16, OC17. The file names of patient OC5 images indicate two tumor sites: OC5_DM (DM – diaphragmatic metastasis) and OC5_OV (OV – ovary). These tissues have been analyzed at various conditions as indicated in the name of each image file (see the following File naming rules section). _Folder De_Luise_D2-40.zip contains 8 immunohistochemistry images from D2-40 marked tissues deriving from 6 patients: OC4, OC5, OC7, OC11, OC14, OC17. These tissues have been analyzed at two different conditions, as indicated in the name of each image file (see the following File naming rules section). _The files in .txt format contain the scripts and the relative classifiers to analyze the tissues marked with hematoxylin/eosin (Neoplastic_cells_classification_from_HE.txt), ⍺SMA (aSMA_cells_classification_and_count.txt), Ki67/ECad (Ki67_ECAD.txt), PAX8 (PAX8_nuclei_area_measurements.txt), CD45 (CD45_cells_classification_and_count.txt), using QuPath (https://github.com/qupath/qupath). File naming rules In general, the image files were named in the following way: ____. Info in the file name Tag in the file name Description patient ID OCX 14 patients (X = 1, 2, 3, 4, 5, 6, 7, 8, 11, 13, 14, 15, 16, 17) tumor site DM diaphragmatic metastasis OV ovary OM omental metastasis marker HE hematoxylin and eosin aSMA_CD31 Alpha smooth muscle actin (αSMA) and CD31 Ki67_ECAD Ki67 and E-cadherin (ECAD) PAX8 Paired box gene 8 CD45 - D2-40 Podoplanin tissue condition Fresh_d0 non-cultured fresh OC tissue Fresh_Pd6 fresh OC tissue cultured in U-CUP bioreactor in perfusion for 6 days Fresh_Sd6 fresh OC tissue cultured for 6 days in static conditions SF_d0 non-cultured slow frozen OC tissue SF_Pd6 slow frozen OC tissue cultured in U-CUP bioreactor in perfusion for 6 days SF_Pd6_SCT slow frozen tissues cultured in U-CUP bioreaction in perfusion for 6 days, in the presence of a combination of carboplatin (70 μM) and paclitaxel (100 nM) mimicking a cycle of standard chemotherapy (SCT) SF_Pd6_UT slow frozen tissues cultured for 6 days in U-CUP bioreaction in perfusion, in absence of treatment that mimicks the standard chemotherapy (UT, untreated) further information ROI region of interest 1, 2,... to differentiate images of the same sample File specifics _.ndpi files can be opened using NDP.view2 (https://www.hamamatsu.com/eu/en/product/life-science-and-medical-systems/digital-slide-scanner/U12388-01.html) or with QuPath (release 0.4.3) _.ndpi, .ome.tiff / .ome.tif, and .tif files can be opened using QuPath (https://github.com/qupath/qupath) Notes The data included in this dataset are presented in the following publication: De Luise, M., Kurelac, I., Coluccelli, S. et al. Perfusion-based ex vivo culture of frozen ovarian cancer tissues with preserved tumor microenvironment. npj Precis. Onc. 9, 152 (2025). https://doi.org/10.1038/s41698-025-00941-6