Raman spectra of rat thymus tissue
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----------------------------------------------------------------------------------------------------------------------------------------Raman spectra of rat thymus tissue---------------------------------------------------------------------------------------------------------------------------------------- * ReadMe version: 1.2 (2026-06-03)* Dataset version: 1.1 (2026-06-03)* Dataset DOI: 10.5281/zenodo.18989675 --------------------------------------------------------------------CONTACT--------------------------------------------------------------------* Daniela Janstova* janstovd@vscht.cz* 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 (Investigation, Methodology) * Daniela Janstova (0000-0002-0300-3878), Dept. of Mathematics, Cybernetics and Informatics, Faculty of Chemical Engineering, University of chemistry and Technology, Prague (Conceptualization, Formal analysis, Funding acquisition, Investigation, Methodology, Project Administration, Software, Visualization) * Jan Valis (0000-0003-0349-6868), Dept. of Analytical Chemistry. Faculty of Chemical Engineering, University of chemistry and Technology, Prague (Conceptualization, Data curation, Investigation, Methodology) * Marcela Dendisova (0000-0002-5895-243X), Dept. of Physical Chemistry. Faculty of Chemical Engineering, University of chemistry and Technology, Prague (Resources - HW, Supervision) * Jan Mares (0000-0003-4693-2519), Dept. of Mathematics, Cybernetics and Informatics, Faculty of Chemical Engineering, University of chemistry and Technology, Prague (Resources - HW&SW, Supervision) ______Contributors______* Veronika Spisska (0000-0003-2339-4906), Dept. of Physiology, Faculty of Science, Charles University (Resources - samples) --------------------------------------------------------------------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│── 000_SampleAnotation.csv├── 001_Data_Spectra_Raw.zip│ ├── Rat001_Thymus_Normal_60um_20250325_40a_5s_50pct_map_10x6_0_X_66.457_Y_14.7298_Time_0.txt│ ├── ...(1046x)│ ├── Rat003_Thymus_Tumour_60um_20260311_40a_5s_50pct_out_map_10x5_49__X_982.444__Y_727.272__Time_10690.txt├── 002_Data_Pictures│ ├── Rat001_Thymus_Normal_60um_20250925_photo_modified.bmp│ ├── ...(12x)│ └── Rat003_Thymus_Tumour_60um_20260302_photo.jpg --------------------------------------------------------------------FILENAME STRUCTURE - IN 001_Data_Spectra_Raw--------------------------------------------------------------------* Rat_Sample_Diagnosis_CutThickness_YYYYMMDD_[description] - Rat ('Rat' and 3 character number) - Sample (Thymus) - Diagnosis (Normal or Tumour) - 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) * e.g.: Rat001_Thymus_Normal_60um_20250810_40a_5s_50pct_map_20x15_43_X_831.457_Y_19.549_Time_1311 - Rat = 001 - 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 (1000 mW at source, 30 mW on sample) - Map dimension = 20x15 - Map Iteration = 43 - X coordinates = X_831.457 - Y coordinates = Y_19.549 - TimeOfMeasurement = 1311 s from the start --------------------------------------------------------------------FILENAME STRUCTURE - IN 002_Data_Pictures--------------------------------------------------------------------* Rat_Sample_Diagnosis_CutThickness_YYYYMMDD_photo_[description] - Rat ('Rat' and 3 character number) - Sample (Thymus) - Diagnosis (Normal or Tumour) - Cut thickness (um) - Date of measurement = YYYYMMDD * Description for Microscopic Pictures: - before = photos taken before measurements - after = photos taken after measurements - modified = photos with visualisation of the measured areas - IntensityAtPoint = photos with visualisation of the signal intensity --------------------------------------------------------------------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.) delimiter: tabulator* Microscopic pictures original formates: .BMP, or .JPG --------------------------------------------------------------------DATASET CHANGHE LOG--------------------------------------------------------------------* v 1.0 Original version with 727 spectra and 8 pictures* v 1.1 Updated ReadMe, files renamed to contain rat ID, 1048 spectra and 14 pictures
# 大鼠胸腺组织拉曼光谱（Raman spectra）数据集 * ReadMe版本：1.2（2026-06-03）* 数据集版本：1.1（2026-06-03）* 数据集DOI：10.5281/zenodo.18989675 --------------------------------------------------------------------联系信息-------------------------------------------------------------------- * 丹妮拉·扬斯托娃（Daniela Janstova） * janstovd@vscht.cz * ORCID：0000-0002-0300-3878 * 布拉格化学与技术大学化学工程学院分析化学系 * 捷克布拉格6区，Technicka 5号，166 28 ______创作者______ * 马泰什·加诺尔（Matyas Garnol，ORCID：0009-0006-8397-1364），布拉格化学与技术大学化学工程学院分析化学系（调研与实验实施、方法学设计） * 丹妮拉·扬斯托娃（Daniela Janstova，ORCID：0000-0002-0300-3878），布拉格化学与技术大学化学工程学院数学、控制论与信息学系（概念设计、形式分析、项目资助获取、调研与实验实施、方法学设计、项目管理、软件开发、可视化） * 扬·瓦利斯（Jan Valis，ORCID：0000-0003-0349-6868），布拉格化学与技术大学化学工程学院分析化学系（概念设计、数据管理、调研与实验实施、方法学设计） * 马尔塞拉·登迪索娃（Marcela Dendisova，ORCID：0000-0002-5895-243X），布拉格化学与技术大学化学工程学院物理化学系（硬件资源、监督指导） * 扬·马雷斯（Jan Mares，ORCID：0000-0003-4693-2519），布拉格化学与技术大学化学工程学院数学、控制论与信息学系（软硬件资源、监督指导） ______贡献者______ * 维罗妮卡·斯皮斯卡（Veronika Spisska，ORCID：0000-0003-2339-4906），布拉格查理大学理学院生理学系（样本资源） --------------------------------------------------------------------数据获取与访问说明-------------------------------------------------------------------- * 本数据集可通过上述DOI公开获取。 --------------------------------------------------------------------许可协议-------------------------------------------------------------------- ______ReadMe文件许可______ * 扬·瓦利斯创作的ReadMe文件采用CC BY 4.0许可协议授权。 * 许可协议详情：https://creativecommons.org/licenses/by/4.0/ ______数据集许可______ * 马泰什·加诺尔、丹妮拉·扬斯托娃、扬·瓦利斯、马尔塞拉·登迪索娃与扬·马雷斯创作的《大鼠胸腺组织拉曼光谱》数据集采用CC BY 4.0许可协议授权。 * 许可协议详情：https://creativecommons.org/licenses/by/4.0/ --------------------------------------------------------------------数据集描述与实验方法-------------------------------------------------------------------- ______数据集概况______ 拉曼光谱（Raman spectra）是一种高效、无需标记的生物组织分子表征技术，在组织诊断领域具有巨大的应用潜力。本数据集提供了在近天然条件下（未固定、未染色的冰冻切片）采集的大鼠胸腺拉曼光谱数据，涵盖正常健康组织与癌性组织样本，属于带标注数据集，可用于训练并评估生物样本拉曼光谱分类所需的预处理方法与机器学习方法。 ______伦理声明______ 所有实验操作严格遵循美国国立卫生研究院《实验动物护理与使用指南》，并符合捷克共和国《动物保护法》。本实验方案已获捷克共和国教育、青年与体育部批准（批准号：MSMT-31592/2019-4，2019年12月2日）。 ______样本来源与制备______ 胸腺组织取自3只Wistar大鼠（Rattus norvegicus domestica，Velaz有限公司，捷克布拉格），实验工作在布拉格查理大学理学院开展。动物处死后迅速解剖分离胸腺，切除后立即置于干冰（-78℃）中快速冷冻，以防止酶解降解并保留天然生化组成。完全冷冻后，样本转移至无菌微量离心管中，于-80℃保存待用。 将冷冻胸腺组织包埋于Tissue-Tek OCT冰冻包埋剂（日本Sakura Finetek公司）中，固定于金属样本托上。使用徕卡CM1950冰冻切片机（德国徕卡显微系统公司）在约-20℃条件下进行冰冻切片，60μm厚度的切片可在不破坏切片完整性的前提下获得最高信噪比。制备好的冰冻切片立即置于-80℃保存，直至拉曼光谱采集。光谱采集前，将切片置于室温实验室环境中平衡至室温。 ______数据采集方法______ 采用inVia拉曼显微镜（英国Renishaw公司）采集胸腺组织的拉曼光谱，该仪器配备785nm二极管激光器（输出最大功率1000mW，使用100×物镜时样本端功率为30mW）与热电冷却CCD探测器，光谱分辨率约为2cm⁻¹。采集参数设置为：样本端激光功率15mW，曝光时间5s，累积次数40次（总积分时间200s）。光谱采集前，以520.7cm⁻¹处的特征硅拉曼位移峰对光谱仪进行校准，确保光谱精度。按照预设的采集策略，从每个组织切片的多个空间分布位置采集光谱，以最小化空间采样偏差。所有测量均在离体近天然条件下开展，未进行化学固定、染色、脱水或其他额外化学处理，尽可能减少对样本固有生化组成的潜在改变。 ______数据处理方法______ 本数据集仅包含原始数据，未进行任何处理，故未描述相关处理方法。 --------------------------------------------------------------------数据集结构-------------------------------------------------------------------- │── 000_ReadMe.txt │── 000_SampleAnotation.csv ├── 001_Data_Spectra_Raw.zip │ ├── Rat001_Thymus_Normal_60um_20250325_40a_5s_50pct_map_10x6_0_X_66.457_Y_14.7298_Time_0.txt │ ├── ...(共1046个文件) │ ├── Rat003_Thymus_Tumour_60um_20260311_40a_5s_50pct_out_map_10x5_49__X_982.444__Y_727.272__Time_10690.txt ├── 002_Data_Pictures │ ├── Rat001_Thymus_Normal_60um_20250925_photo_modified.bmp │ ├── ...(共12个文件) │ └── Rat003_Thymus_Tumour_60um_20260302_photo.jpg --------------------------------------------------------------------001_Data_Spectra_Raw 文件夹内文件名结构-------------------------------------------------------------------- * 命名规则：大鼠编号_样本类型_诊断结果_切片厚度_测量日期_[补充描述] - 大鼠编号：格式为“Rat”加3位数字 - 样本类型：固定为Thymus（胸腺） - 诊断结果：Normal（正常）或Tumour（肿瘤） - 切片厚度：单位为μm - 测量日期：格式为YYYYMMDD * 拉曼光谱文件补充描述字段：[累积次数_单次曝光时间_激光功率_扫描维度_扫描迭代次数_X坐标_Y坐标_测量起始时长] - 累积次数：用于平均计算的累积扫描次数 - 单次曝光时间：单位为秒(s) - 激光功率：以满功率的百分比表示（激光器满输出功率1000mW，样本端满功率30mW） - 扫描维度：扫描区域的网格尺寸 - 扫描迭代次数：当前扫描的迭代编号 - X坐标：采样点的X坐标 - Y坐标：采样点的Y坐标 - 测量起始时长：从扫描开始至当前采样的时长，单位为秒(s) * 示例：Rat001_Thymus_Normal_60um_20250810_40a_5s_50pct_map_20x15_43_X_831.457_Y_19.549_Time_1311 - 大鼠编号：001 - 样本类型：胸腺 - 切片厚度：60μm - 诊断结果：正常 - 测量日期：20250810 - 累积次数：40次 - 单次曝光时间：5s - 激光功率：50%满功率（激光器满输出1000mW，样本端满功率30mW） - 扫描维度：20×15 - 扫描迭代次数：43 - X坐标：831.457 - Y坐标：19.549 - 测量起始时长：扫描开始后1311秒 --------------------------------------------------------------------002_Data_Pictures 文件夹内文件名结构-------------------------------------------------------------------- * 命名规则：大鼠编号_样本类型_诊断结果_切片厚度_测量日期_photo_[补充描述] - 大鼠编号：格式为“Rat”加3位数字 - 样本类型：固定为Thymus（胸腺） - 诊断结果：Normal（正常）或Tumour（肿瘤） - 切片厚度：单位为μm - 测量日期：格式为YYYYMMDD * 显微照片补充描述字段说明： - before：采集前拍摄的照片 - after：采集后拍摄的照片 - modified：标注了采样区域的可视化照片 - IntensityAtPoint：显示信号强度分布的可视化照片 --------------------------------------------------------------------文件类型与格式、维度与单位-------------------------------------------------------------------- * 拉曼光谱文件 - 转换后格式：.TXT - 横轴/第一列：拉曼位移（cm⁻¹） - 纵轴/第二列：信号强度（任意单位，a.u.） - 分隔符：制表符 * 显微照片 - 原始格式：.BMP 或 .JPG --------------------------------------------------------------------数据集更新日志-------------------------------------------------------------------- * v1.0：初始版本，包含727条光谱与8张照片 * v1.1：更新了ReadMe文件，对文件重命名以包含大鼠编号，现包含1048条光谱与14张照片
