├── LICENSE └── README.md /LICENSE: -------------------------------------------------------------------------------- 1 | Attribution-NonCommercial 4.0 International 2 | 3 | ======================================================================= 4 | 5 | Creative Commons Corporation ("Creative Commons") is not a law firm and 6 | does not provide legal services or legal advice. Distribution of 7 | Creative Commons public licenses does not create a lawyer-client or 8 | other relationship. Creative Commons makes its licenses and related 9 | information available on an "as-is" basis. Creative Commons gives no 10 | warranties regarding its licenses, any material licensed under their 11 | terms and conditions, or any related information. Creative Commons 12 | disclaims all liability for damages resulting from their use to the 13 | fullest extent possible. 14 | 15 | Using Creative Commons Public Licenses 16 | 17 | Creative Commons public licenses provide a standard set of terms and 18 | conditions that creators and other rights holders may use to share 19 | original works of authorship and other material subject to copyright 20 | and certain other rights specified in the public license below. The 21 | following considerations are for informational purposes only, are not 22 | exhaustive, and do not form part of our licenses. 23 | 24 | Considerations for licensors: Our public licenses are 25 | intended for use by those authorized to give the public 26 | permission to use material in ways otherwise restricted by 27 | copyright and certain other rights. Our licenses are 28 | irrevocable. Licensors should read and understand the terms 29 | and conditions of the license they choose before applying it. 30 | Licensors should also secure all rights necessary before 31 | applying our licenses so that the public can reuse the 32 | material as expected. Licensors should clearly mark any 33 | material not subject to the license. This includes other CC- 34 | licensed material, or material used under an exception or 35 | limitation to copyright. More considerations for licensors: 36 | wiki.creativecommons.org/Considerations_for_licensors 37 | 38 | Considerations for the public: By using one of our public 39 | licenses, a licensor grants the public permission to use the 40 | licensed material under specified terms and conditions. If 41 | the licensor's permission is not necessary for any reason--for 42 | example, because of any applicable exception or limitation to 43 | copyright--then that use is not regulated by the license. Our 44 | licenses grant only permissions under copyright and certain 45 | other rights that a licensor has authority to grant. Use of 46 | the licensed material may still be restricted for other 47 | reasons, including because others have copyright or other 48 | rights in the material. A licensor may make special requests, 49 | such as asking that all changes be marked or described. 50 | Although not required by our licenses, you are encouraged to 51 | respect those requests where reasonable. More considerations 52 | for the public: 53 | wiki.creativecommons.org/Considerations_for_licensees 54 | 55 | ======================================================================= 56 | 57 | Creative Commons Attribution-NonCommercial 4.0 International Public 58 | License 59 | 60 | By exercising the Licensed Rights (defined below), You accept and agree 61 | to be bound by the terms and conditions of this Creative Commons 62 | Attribution-NonCommercial 4.0 International Public License ("Public 63 | License"). To the extent this Public License may be interpreted as a 64 | contract, You are granted the Licensed Rights in consideration of Your 65 | acceptance of these terms and conditions, and the Licensor grants You 66 | such rights in consideration of benefits the Licensor receives from 67 | making the Licensed Material available under these terms and 68 | conditions. 69 | 70 | 71 | Section 1 -- Definitions. 72 | 73 | a. Adapted Material means material subject to Copyright and Similar 74 | Rights that is derived from or based upon the Licensed Material 75 | and in which the Licensed Material is translated, altered, 76 | arranged, transformed, or otherwise modified in a manner requiring 77 | permission under the Copyright and Similar Rights held by the 78 | Licensor. For purposes of this Public License, where the Licensed 79 | Material is a musical work, performance, or sound recording, 80 | Adapted Material is always produced where the Licensed Material is 81 | synched in timed relation with a moving image. 82 | 83 | b. Adapter's License means the license You apply to Your Copyright 84 | and Similar Rights in Your contributions to Adapted Material in 85 | accordance with the terms and conditions of this Public License. 86 | 87 | c. Copyright and Similar Rights means copyright and/or similar rights 88 | closely related to copyright including, without limitation, 89 | performance, broadcast, sound recording, and Sui Generis Database 90 | Rights, without regard to how the rights are labeled or 91 | categorized. For purposes of this Public License, the rights 92 | specified in Section 2(b)(1)-(2) are not Copyright and Similar 93 | Rights. 94 | d. Effective Technological Measures means those measures that, in the 95 | absence of proper authority, may not be circumvented under laws 96 | fulfilling obligations under Article 11 of the WIPO Copyright 97 | Treaty adopted on December 20, 1996, and/or similar international 98 | agreements. 99 | 100 | e. Exceptions and Limitations means fair use, fair dealing, and/or 101 | any other exception or limitation to Copyright and Similar Rights 102 | that applies to Your use of the Licensed Material. 103 | 104 | f. Licensed Material means the artistic or literary work, database, 105 | or other material to which the Licensor applied this Public 106 | License. 107 | 108 | g. Licensed Rights means the rights granted to You subject to the 109 | terms and conditions of this Public License, which are limited to 110 | all Copyright and Similar Rights that apply to Your use of the 111 | Licensed Material and that the Licensor has authority to license. 112 | 113 | h. Licensor means the individual(s) or entity(ies) granting rights 114 | under this Public License. 115 | 116 | i. NonCommercial means not primarily intended for or directed towards 117 | commercial advantage or monetary compensation. For purposes of 118 | this Public License, the exchange of the Licensed Material for 119 | other material subject to Copyright and Similar Rights by digital 120 | file-sharing or similar means is NonCommercial provided there is 121 | no payment of monetary compensation in connection with the 122 | exchange. 123 | 124 | j. Share means to provide material to the public by any means or 125 | process that requires permission under the Licensed Rights, such 126 | as reproduction, public display, public performance, distribution, 127 | dissemination, communication, or importation, and to make material 128 | available to the public including in ways that members of the 129 | public may access the material from a place and at a time 130 | individually chosen by them. 131 | 132 | k. Sui Generis Database Rights means rights other than copyright 133 | resulting from Directive 96/9/EC of the European Parliament and of 134 | the Council of 11 March 1996 on the legal protection of databases, 135 | as amended and/or succeeded, as well as other essentially 136 | equivalent rights anywhere in the world. 137 | 138 | l. You means the individual or entity exercising the Licensed Rights 139 | under this Public License. Your has a corresponding meaning. 140 | 141 | 142 | Section 2 -- Scope. 143 | 144 | a. License grant. 145 | 146 | 1. Subject to the terms and conditions of this Public License, 147 | the Licensor hereby grants You a worldwide, royalty-free, 148 | non-sublicensable, non-exclusive, irrevocable license to 149 | exercise the Licensed Rights in the Licensed Material to: 150 | 151 | a. reproduce and Share the Licensed Material, in whole or 152 | in part, for NonCommercial purposes only; and 153 | 154 | b. produce, reproduce, and Share Adapted Material for 155 | NonCommercial purposes only. 156 | 157 | 2. Exceptions and Limitations. For the avoidance of doubt, where 158 | Exceptions and Limitations apply to Your use, this Public 159 | License does not apply, and You do not need to comply with 160 | its terms and conditions. 161 | 162 | 3. Term. The term of this Public License is specified in Section 163 | 6(a). 164 | 165 | 4. Media and formats; technical modifications allowed. The 166 | Licensor authorizes You to exercise the Licensed Rights in 167 | all media and formats whether now known or hereafter created, 168 | and to make technical modifications necessary to do so. The 169 | Licensor waives and/or agrees not to assert any right or 170 | authority to forbid You from making technical modifications 171 | necessary to exercise the Licensed Rights, including 172 | technical modifications necessary to circumvent Effective 173 | Technological Measures. For purposes of this Public License, 174 | simply making modifications authorized by this Section 2(a) 175 | (4) never produces Adapted Material. 176 | 177 | 5. Downstream recipients. 178 | 179 | a. Offer from the Licensor -- Licensed Material. Every 180 | recipient of the Licensed Material automatically 181 | receives an offer from the Licensor to exercise the 182 | Licensed Rights under the terms and conditions of this 183 | Public License. 184 | 185 | b. No downstream restrictions. You may not offer or impose 186 | any additional or different terms or conditions on, or 187 | apply any Effective Technological Measures to, the 188 | Licensed Material if doing so restricts exercise of the 189 | Licensed Rights by any recipient of the Licensed 190 | Material. 191 | 192 | 6. No endorsement. Nothing in this Public License constitutes or 193 | may be construed as permission to assert or imply that You 194 | are, or that Your use of the Licensed Material is, connected 195 | with, or sponsored, endorsed, or granted official status by, 196 | the Licensor or others designated to receive attribution as 197 | provided in Section 3(a)(1)(A)(i). 198 | 199 | b. Other rights. 200 | 201 | 1. Moral rights, such as the right of integrity, are not 202 | licensed under this Public License, nor are publicity, 203 | privacy, and/or other similar personality rights; however, to 204 | the extent possible, the Licensor waives and/or agrees not to 205 | assert any such rights held by the Licensor to the limited 206 | extent necessary to allow You to exercise the Licensed 207 | Rights, but not otherwise. 208 | 209 | 2. Patent and trademark rights are not licensed under this 210 | Public License. 211 | 212 | 3. To the extent possible, the Licensor waives any right to 213 | collect royalties from You for the exercise of the Licensed 214 | Rights, whether directly or through a collecting society 215 | under any voluntary or waivable statutory or compulsory 216 | licensing scheme. In all other cases the Licensor expressly 217 | reserves any right to collect such royalties, including when 218 | the Licensed Material is used other than for NonCommercial 219 | purposes. 220 | 221 | 222 | Section 3 -- License Conditions. 223 | 224 | Your exercise of the Licensed Rights is expressly made subject to the 225 | following conditions. 226 | 227 | a. Attribution. 228 | 229 | 1. If You Share the Licensed Material (including in modified 230 | form), You must: 231 | 232 | a. retain the following if it is supplied by the Licensor 233 | with the Licensed Material: 234 | 235 | i. identification of the creator(s) of the Licensed 236 | Material and any others designated to receive 237 | attribution, in any reasonable manner requested by 238 | the Licensor (including by pseudonym if 239 | designated); 240 | 241 | ii. a copyright notice; 242 | 243 | iii. a notice that refers to this Public License; 244 | 245 | iv. a notice that refers to the disclaimer of 246 | warranties; 247 | 248 | v. a URI or hyperlink to the Licensed Material to the 249 | extent reasonably practicable; 250 | 251 | b. indicate if You modified the Licensed Material and 252 | retain an indication of any previous modifications; and 253 | 254 | c. indicate the Licensed Material is licensed under this 255 | Public License, and include the text of, or the URI or 256 | hyperlink to, this Public License. 257 | 258 | 2. You may satisfy the conditions in Section 3(a)(1) in any 259 | reasonable manner based on the medium, means, and context in 260 | which You Share the Licensed Material. For example, it may be 261 | reasonable to satisfy the conditions by providing a URI or 262 | hyperlink to a resource that includes the required 263 | information. 264 | 265 | 3. If requested by the Licensor, You must remove any of the 266 | information required by Section 3(a)(1)(A) to the extent 267 | reasonably practicable. 268 | 269 | 4. If You Share Adapted Material You produce, the Adapter's 270 | License You apply must not prevent recipients of the Adapted 271 | Material from complying with this Public License. 272 | 273 | 274 | Section 4 -- Sui Generis Database Rights. 275 | 276 | Where the Licensed Rights include Sui Generis Database Rights that 277 | apply to Your use of the Licensed Material: 278 | 279 | a. for the avoidance of doubt, Section 2(a)(1) grants You the right 280 | to extract, reuse, reproduce, and Share all or a substantial 281 | portion of the contents of the database for NonCommercial purposes 282 | only; 283 | 284 | b. if You include all or a substantial portion of the database 285 | contents in a database in which You have Sui Generis Database 286 | Rights, then the database in which You have Sui Generis Database 287 | Rights (but not its individual contents) is Adapted Material; and 288 | 289 | c. You must comply with the conditions in Section 3(a) if You Share 290 | all or a substantial portion of the contents of the database. 291 | 292 | For the avoidance of doubt, this Section 4 supplements and does not 293 | replace Your obligations under this Public License where the Licensed 294 | Rights include other Copyright and Similar Rights. 295 | 296 | 297 | Section 5 -- Disclaimer of Warranties and Limitation of Liability. 298 | 299 | a. UNLESS OTHERWISE SEPARATELY UNDERTAKEN BY THE LICENSOR, TO THE 300 | EXTENT POSSIBLE, THE LICENSOR OFFERS THE LICENSED MATERIAL AS-IS 301 | AND AS-AVAILABLE, AND MAKES NO REPRESENTATIONS OR WARRANTIES OF 302 | ANY KIND CONCERNING THE LICENSED MATERIAL, WHETHER EXPRESS, 303 | IMPLIED, STATUTORY, OR OTHER. THIS INCLUDES, WITHOUT LIMITATION, 304 | WARRANTIES OF TITLE, MERCHANTABILITY, FITNESS FOR A PARTICULAR 305 | PURPOSE, NON-INFRINGEMENT, ABSENCE OF LATENT OR OTHER DEFECTS, 306 | ACCURACY, OR THE PRESENCE OR ABSENCE OF ERRORS, WHETHER OR NOT 307 | KNOWN OR DISCOVERABLE. WHERE DISCLAIMERS OF WARRANTIES ARE NOT 308 | ALLOWED IN FULL OR IN PART, THIS DISCLAIMER MAY NOT APPLY TO YOU. 309 | 310 | b. TO THE EXTENT POSSIBLE, IN NO EVENT WILL THE LICENSOR BE LIABLE 311 | TO YOU ON ANY LEGAL THEORY (INCLUDING, WITHOUT LIMITATION, 312 | NEGLIGENCE) OR OTHERWISE FOR ANY DIRECT, SPECIAL, INDIRECT, 313 | INCIDENTAL, CONSEQUENTIAL, PUNITIVE, EXEMPLARY, OR OTHER LOSSES, 314 | COSTS, EXPENSES, OR DAMAGES ARISING OUT OF THIS PUBLIC LICENSE OR 315 | USE OF THE LICENSED MATERIAL, EVEN IF THE LICENSOR HAS BEEN 316 | ADVISED OF THE POSSIBILITY OF SUCH LOSSES, COSTS, EXPENSES, OR 317 | DAMAGES. WHERE A LIMITATION OF LIABILITY IS NOT ALLOWED IN FULL OR 318 | IN PART, THIS LIMITATION MAY NOT APPLY TO YOU. 319 | 320 | c. The disclaimer of warranties and limitation of liability provided 321 | above shall be interpreted in a manner that, to the extent 322 | possible, most closely approximates an absolute disclaimer and 323 | waiver of all liability. 324 | 325 | 326 | Section 6 -- Term and Termination. 327 | 328 | a. This Public License applies for the term of the Copyright and 329 | Similar Rights licensed here. However, if You fail to comply with 330 | this Public License, then Your rights under this Public License 331 | terminate automatically. 332 | 333 | b. Where Your right to use the Licensed Material has terminated under 334 | Section 6(a), it reinstates: 335 | 336 | 1. automatically as of the date the violation is cured, provided 337 | it is cured within 30 days of Your discovery of the 338 | violation; or 339 | 340 | 2. upon express reinstatement by the Licensor. 341 | 342 | For the avoidance of doubt, this Section 6(b) does not affect any 343 | right the Licensor may have to seek remedies for Your violations 344 | of this Public License. 345 | 346 | c. For the avoidance of doubt, the Licensor may also offer the 347 | Licensed Material under separate terms or conditions or stop 348 | distributing the Licensed Material at any time; however, doing so 349 | will not terminate this Public License. 350 | 351 | d. Sections 1, 5, 6, 7, and 8 survive termination of this Public 352 | License. 353 | 354 | 355 | Section 7 -- Other Terms and Conditions. 356 | 357 | a. The Licensor shall not be bound by any additional or different 358 | terms or conditions communicated by You unless expressly agreed. 359 | 360 | b. Any arrangements, understandings, or agreements regarding the 361 | Licensed Material not stated herein are separate from and 362 | independent of the terms and conditions of this Public License. 363 | 364 | 365 | Section 8 -- Interpretation. 366 | 367 | a. For the avoidance of doubt, this Public License does not, and 368 | shall not be interpreted to, reduce, limit, restrict, or impose 369 | conditions on any use of the Licensed Material that could lawfully 370 | be made without permission under this Public License. 371 | 372 | b. To the extent possible, if any provision of this Public License is 373 | deemed unenforceable, it shall be automatically reformed to the 374 | minimum extent necessary to make it enforceable. If the provision 375 | cannot be reformed, it shall be severed from this Public License 376 | without affecting the enforceability of the remaining terms and 377 | conditions. 378 | 379 | c. No term or condition of this Public License will be waived and no 380 | failure to comply consented to unless expressly agreed to by the 381 | Licensor. 382 | 383 | d. Nothing in this Public License constitutes or may be interpreted 384 | as a limitation upon, or waiver of, any privileges and immunities 385 | that apply to the Licensor or You, including from the legal 386 | processes of any jurisdiction or authority. 387 | 388 | ======================================================================= 389 | 390 | Creative Commons is not a party to its public 391 | licenses. Notwithstanding, Creative Commons may elect to apply one of 392 | its public licenses to material it publishes and in those instances 393 | will be considered the “Licensor.” The text of the Creative Commons 394 | public licenses is dedicated to the public domain under the CC0 Public 395 | Domain Dedication. Except for the limited purpose of indicating that 396 | material is shared under a Creative Commons public license or as 397 | otherwise permitted by the Creative Commons policies published at 398 | creativecommons.org/policies, Creative Commons does not authorize the 399 | use of the trademark "Creative Commons" or any other trademark or logo 400 | of Creative Commons without its prior written consent including, 401 | without limitation, in connection with any unauthorized modifications 402 | to any of its public licenses or any other arrangements, 403 | understandings, or agreements concerning use of licensed material. For 404 | the avoidance of doubt, this paragraph does not form part of the 405 | public licenses. 406 | 407 | Creative Commons may be contacted at creativecommons.org. 408 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # SPIDER: A Multi-Organ Supervised Pathology Dataset and Baseline Models 2 | 3 | ## Overview 4 | SPIDER (**S**upervised **P**athology **I**mage-**DE**scription **R**epository) is a large, high-quality, and diverse patch-level dataset designed to advance AI-driven computational pathology. It provides multi-organ coverage, expert-annotated labels, and strong baseline models to support research and development in digital pathology. 5 | 6 | This repository serves as a central hub for accessing the SPIDER datasets, pre-trained models, and related resources. 7 | 8 | --- 9 | 10 | ## 📄 Paper 11 | For a detailed description of SPIDER, methodology, and benchmark results, refer to our research paper: 12 | 13 | 📄 **SPIDER: A Comprehensive Multi-Organ Supervised Pathology Dataset and Baseline Models** 14 | [View on arXiv](https://arxiv.org/abs/2503.02876) 15 | 16 | --- 17 | 18 | ## Resources 19 | 20 | ### 📂 Datasets 21 | SPIDER consists of four organ-specific datasets. Available for download from [Hugging Face Hub](https://huggingface.co/histai) 🤗: 22 | - [SPIDER-Skin](https://huggingface.co/datasets/histai/SPIDER-skin) 23 | - [SPIDER-Colorectal](https://huggingface.co/datasets/histai/SPIDER-colorectal) 24 | - [SPIDER-Thorax](https://huggingface.co/datasets/histai/SPIDER-thorax) 25 | - [SPIDER-Breast](https://huggingface.co/datasets/histai/SPIDER-breast) 26 | 27 | Each dataset contains: 28 | - **224×224 central patches** with expert-verified class labels 29 | - **24 surrounding context patches** forming a **1120×1120 composite region** 30 | - **20X magnification** for high-detail analysis 31 | - Train-test splits ensuring robust benchmarking 32 | 33 | 📌 *See individual dataset pages for more details.* 34 | 35 | ### 🤖 Pretrained Models 36 | Baseline models trained on the SPIDER datasets using the **Hibou-L** foundation model with an attention-based classification head. Available for download from [Hugging Face Hub](https://huggingface.co/histai) 🤗: 37 | - [SPIDER-Skin Model](https://huggingface.co/histai/SPIDER-skin-model) 38 | - [SPIDER-Colorectal Model](https://huggingface.co/histai/SPIDER-colorectal-model) 39 | - [SPIDER-Thorax Model](https://huggingface.co/histai/SPIDER-thorax-model) 40 | - [SPIDER-Breast Model](https://huggingface.co/histai/SPIDER-breast-model) 41 | 42 | Each model supports: 43 | - Patch-level classification with multi-class labels 44 | - **Improved accuracy using surrounding context patches** 45 | - **Easy deployment** for pathology AI applications 46 | 47 | 📌 *See individual model pages for inference instructions.* 48 | 49 | --- 50 | 51 | ## 🔧 Getting Started 52 | ### 🛠 Using the Dataset 53 | Download any SPIDER dataset using `huggingface_hub`: 54 | ```python 55 | from huggingface_hub import snapshot_download 56 | snapshot_download(repo_id="histai/SPIDER-colorectal", repo_type="dataset", local_dir="./spider_colorectal") 57 | ``` 58 | Or clone directly using Git: 59 | ```bash 60 | git lfs install 61 | git clone https://huggingface.co/datasets/histai/SPIDER-colorectal 62 | ``` 63 | Extract dataset files: 64 | ```bash 65 | cat spider-colorectal.tar.* | tar -xvf - 66 | ``` 67 | 68 | ### 🤖 Using the Model 69 | Load a pretrained model for inference: 70 | ```python 71 | from transformers import AutoModel, AutoProcessor 72 | from PIL import Image 73 | 74 | model = AutoModel.from_pretrained("histai/SPIDER-colorectal-model", trust_remote_code=True) 75 | processor = AutoProcessor.from_pretrained("histai/SPIDER-colorectal-model", trust_remote_code=True) 76 | 77 | image = Image.open("path_to_image.png") 78 | inputs = processor(images=image, return_tensors="pt") 79 | outputs = model(**inputs) 80 | print(outputs.predicted_class_names) 81 | ``` 82 | 83 | --- 84 | 85 | ## 📈 Benchmark Results 86 | | Organ | Accuracy | Precision | F1 Score | 87 | |-------------|----------|------------|----------| 88 | | **Skin** | 0.940 | 0.935 | 0.937 | 89 | | **Colorectal** | 0.914 | 0.917 | 0.915 | 90 | | **Thorax** | 0.962 | 0.958 | 0.960 | 91 | | **Breast** | 0.902 | 0.896 | 0.897 | 92 | 93 | --- 94 | 95 | ## 🔗 More Information 96 | - [Hugging Face Profile](https://huggingface.co/histai) 97 | - [GitHub Repository](https://github.com/HistAI/SPIDER) 98 | 99 | --- 100 | 101 | ## 📜 License 102 | This project is licensed under **CC BY-NC 4.0**. The dataset and models are available **for research use only**. 103 | 104 | --- 105 | 106 | ## 📧 Contact 107 | **Authors:** Dmitry Nechaev, Alexey Pchelnikov, Ekaterina Ivanova 108 | 📩 **Emails:** dmitry@hist.ai, alex@hist.ai, kate@hist.ai 109 | 110 | --- 111 | 112 | ## 📖 Citation 113 | If you use SPIDER in your research, please cite: 114 | ```bibtex 115 | @misc{nechaev2025spidercomprehensivemultiorgansupervised, 116 | title={SPIDER: A Comprehensive Multi-Organ Supervised Pathology Dataset and Baseline Models}, 117 | author={Dmitry Nechaev and Alexey Pchelnikov and Ekaterina Ivanova}, 118 | year={2025}, 119 | eprint={2503.02876}, 120 | archivePrefix={arXiv}, 121 | primaryClass={eess.IV}, 122 | url={https://arxiv.org/abs/2503.02876}, 123 | } 124 | ``` 125 | --------------------------------------------------------------------------------