Raman spectra of rat thymus tissue

----------------------------------------------------------------------------------------------------------------------------------------Raman spectra of rat thymus tissue---------------------------------------------------------------------------------------------------------------------------------------- * ReadMe version: 1.1 (2026-03-12)* Dataset version: 1.0 (2025-12-04)* Dataset DOI: 10.5281/zenodo.18989676 --------------------------------------------------------------------CONTACT--------------------------------------------------------------------* Daniela Janstova* [e-mail]* ORCID: 0000-0002-0300-3878* Dept. of . Faculty of Chemical Engineering, University of chemistry and Technology, Prague* Technicka 5, 166 28, Prague 6, Czech Republic ______Creators______* Matyas Garnol (0009-0006-8397-1364), Dept. of Analytical Chemistry. Faculty of Chemical Engineering, University of chemistry and Technology, Prague* Daniela Janstova (0000-0002-0300-3878), Dept. of Mathematics, Cybernetics and Informatics, Faculty of Chemical Engineering, University of chemistry and Technology, Prague* Jan Valis (0000-0003-0349-6868), Dept. of Analytical Chemistry. Faculty of Chemical Engineering, University of chemistry and Technology, Prague* Marcela Dendisova (0000-0002-5895-243X), Dept. of Physical Chemistry. Faculty of Chemical Engineering, University of chemistry and Technology, Prague* Jan Mares (0000-0003-4693-2519), Dept. of Mathematics, Cybernetics and Informatics, Faculty of Chemical Engineering, University of chemistry and Technology, Prague ______Contributors______* Veronika Spisska (0000-0003-2339-4906), Dept. of Physiology, Faculty of Science, Charles University --------------------------------------------------------------------DATA AVAILABILITY AND ACCESS INSTRUCTIONS--------------------------------------------------------------------* The dataset is openly accessible under the DOI listed above. --------------------------------------------------------------------LICENSE--------------------------------------------------------------------______ReadMe file license______* ReadMe by Jan Valis is licensed under CC BY 4.0* Licence information: https://creativecommons.org/licenses/by/4.0/ ______Dataset license______* Dataset Raman spectra of rat thymus tissue by Matyas Garnol, Daniela Janstova, Jan Valis, Marcela Dendisova and Jan Mares is licensed under CC BY 4.0* Licence information: https://creativecommons.org/licenses/by/4.0/ --------------------------------------------------------------------DESCRIPTION AND METHODOLOGY-------------------------------------------------------------------- ______About the dataset______Raman spectroscopy offers a powerful, label-free approach for molecular characterization of biological tissues, with enormous potential for advancing tissue diagnostics. Here, we present a controlled dataset of rat thymus Raman spectra measured under near-native conditions (non-fixed, unstained cryosections). Both normal healthy and cancerous tissue samples were measured. This labeled dataset can be used to train and evaluate pre-processing methods as well as machine-learning methods for classification of Raman spectra of biological samples. ______Ethics______All experimental procedures were conducted in strict accordance with the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health and complied with the Animal Protection Law of the Czech Republic. The experimental protocol was approved by the Ministry of Education, Youth and Sports of the Czech Republic (approval number: MSMT-31592/2019-4, December 2, 2019). ______Sample provenance and preparation______Thymus tissues were obtained from three Wistar rats (Rattus norvegicus domestica, Velaz Ltd., Prague, Czech Republic) as part of the experimental work conducted at the Faculty of Science, Charles University (Prague, CzechRepublic). Animal euthanasia was followed by rapid dissection and isolation of the thymus. Immediately after excision, tissues were snap-frozen on dry ice (−78 °C) to prevent enzymatic degradation and preserve native biochemical composition. After complete freezing, samples were transferred into sterile microcentrifuge tubes and stored at −80 °C until further processing. Frozen thymus tissues were embedded in Tissue-Tek OCT Cryomount compound (Sakura Finetek, Japan) and mounted onto a metal specimen holder. Cryosectioning was performed using a Leica CM1950 cryostat (Leica Microsystems, Germany) at approximately −20 °C. 60 μm thick sections provided the highest signal-to-noise ration without compromising section integrity. Prepared cryosections were immediately stored at −80 °C until Raman measurements. Prior to spectral acquisition, sections were allowed to equilibrate to room temperature under ambient laboratory conditions. ______Methods of data collection______Raman spectra of thymus tissue were acquired using an inVia Raman microscope (Renishaw, UK) equipped with a 785 nm diode laser (max output 1000 mW on output/30 mW on sample with 100× objective), and a thermo-electrically cooled CCD detector. The spectral resolution was approximately 2 cm−1. Acquisition parameters were: 15 mW power on sample, 5 s exposure and 40 accumulations (total integration time 200 s). Prior to spectral acquisition, the spectrometer was calibrated using the characteristic silicon Raman band at 520.7 cm−1 to ensure spectral accuracy. Spectra were collected from multiple spatially distributed positions across each tissue section according to a predefined acquisition strategy to minimize spatial sampling bias. All measurements were performed under ex vivo near-native conditions without chemical fixation, staining, dehydration, or additional chemical treatment, thereby minimizing potential alterations of the intrinsic biochemical composition. ______Methods of data processing______The dataset contains only raw data; therefore, no processing is described. --------------------------------------------------------------------DATASET STRUCTURE--------------------------------------------------------------------│── 000_ReadMe.txt├── 001_Data-Raw_Spectra│ ├── Thymus_normal_60um_20250325_40a_5s_50pct_map_10x6_0_X_66.457_Y_14.7298_Time_0.txt│ ├── ...(725x)│ └── Thymus_tumor_60um_20251204_40a_5s_50pct_out_map_10x10_86__X_801.463__Y_678.283__Time_18633.txt├── 002_Data-Raw_Pictures│ ├── Thymus_normal_60um_20250325_photo.bmp│ ├── ...(6x)│ └── Thymus_tumor_60um_20251204_photo.jpg --------------------------------------------------------------------FILENAME STRUCTURE--------------------------------------------------------------------* Sample_Diagnosis_CutThickness_YYYYMMDD_[description] - Sample (Thymus) - Diagnosis (normal or cancer) - Cut thickness (um) - Date of measurement = YYYYMMDD * Description for Raman spectra: [NoOfAccumulations_AccumulationTime_Power_MapNoXNo_MapIteration_X_coordinates_Y_coordinates_TimeOfMeasurement] - No. of accumulations (for averaging) - Accumulation time (s) - Laser power (% out of 1000 mW on output/30 mW on sample) - Map dimension - Map Iteration - X coordinates - Y coordinates - TimeOfMeasurement (0 on start) * Description for microscopic photos: photo * e.g.: Thymus_normal_60um_20250810_40a_5s_50pct_map_20x15_43_X_831.457_Y_19.549_Time_1311 - Sample = thymus - Cut thickness = 60um = 60 μm - Diagnosis = normal - Date = YYYYMMDD = 20250810 - No. of accumulations (for averaging) = 40a = 40 x - Accumulation time = 5s - Laser power = 50pct = 50 % of maximal power () - Map dimension = 20x15 - Map Iteration = 43 - X coordinates = X_831.457 - Y coordinates = Y_19.549 - TimeOfMeasurement = 1311 s from the start --------------------------------------------------------------------FILE TYPES & FORMATS, AND DIMENSIONS & UNITS--------------------------------------------------------------------* Raman spectra converted format: .TXT horizontal axis/first column: Raman shift (cm^-1) vertical axis/second column: Intensity (a.u.)* Microscopic pictures original formates: .BMP, or .JPG