Add LICENSE file and update README with dataset details and installation instructions

LICENSE

@@ -0,0 +1,367 @@
+Creative Commons Attribution 4.0 International Public License
+
+By exercising the Licensed Rights (defined below), You accept and agree
+to be bound by the terms and conditions of this Creative Commons
+Attribution 4.0 International Public License ("Public License"). To the
+extent this Public License may be interpreted as a contract, You are
+granted the Licensed Rights in consideration of Your acceptance of
+these terms and conditions, and the Licensor grants You such rights in
+consideration of benefits the Licensor receives from making the
+Licensed Material available under these terms and conditions.
+
+=======================================================================
+
+Section 1 -- Definitions.
+
+  a. Adapted Material means material subject to Copyright and Similar
+     Rights that is derived from or based upon the Licensed Material
+     and in which the Licensed Material is translated, altered,
+     arranged, transformed, or otherwise modified in a manner requiring
+     permission under the Copyright and Similar Rights held by the
+     Licensor. For purposes of this Public License, where the Licensed
+     Material is a musical work, performance, or sound recording,
+     Adapted Material is always produced where the Licensed Material is
+     synched in timed relation with a moving image.
+
+  b. Adapter's License means the license You apply to Your Copyright
+     and Similar Rights in Your contributions to Adapted Material in
+     accordance with the terms and conditions of this Public License.
+
+  c. BY-NC-ND means the name of a Creative Commons license indicating
+     the Licensed Rights are limited to NonCommercial purposes and that
+     Adapters may not share Adapted Material.
+
+  d. BY-NC-SA means the name of a Creative Commons license indicating
+     the Licensed Rights are limited to NonCommercial purposes and that
+     Adapters must share Adapted Material under the same or a
+     compatible license.
+
+  e. Copyright and Similar Rights means copyright and/or similar rights
+     closely related to copyright including, without limitation,
+     performance, broadcast, sound recording, and Sui Generis Database
+     Rights, without regard to how the rights are labeled or
+     categorized. For purposes of this Public License, the rights
+     specified in Section 2(b)(1)-(2) are not Copyright and Similar
+     Rights.
+
+  f. Effective Technological Measures means those measures that, in the
+     absence of proper authority, may not be circumvented under laws
+     fulfilling obligations under Article 11 of the WIPO Copyright
+     Treaty adopted on December 20, 1996, and/or similar international
+     agreements.
+
+  g. Exceptions and Limitations means fair use, fair dealing, and/or
+     any other exception or limitation to Copyright and Similar Rights
+     that applies to Your use of the Licensed Material.
+
+  h. Licensed Material means the artistic or literary work, database,
+     or other material to which the Licensor applied this Public
+     License.
+
+  i. Licensed Rights means the rights granted to You subject to the
+     terms and conditions of this Public License, which are limited to
+     all Copyright and Similar Rights that apply to Your use of the
+
+     Licensed Material and that the Licensor has authority to license.
+
+  j. Licensor means the individual(s) or entity(ies) granting rights
+     under this Public License.
+
+  k. NonCommercial means not primarily intended for or directed towards
+     commercial advantage or monetary compensation. For purposes of
+     this Public License, the exchange of the Licensed Material for
+     other material subject to Copyright and Similar Rights by digital
+     file-sharing or similar means is NonCommercial provided there is
+     no payment of monetary compensation in connection with the
+     exchange.
+
+  l. Share means to provide material to the public by any means or
+     process that requires permission under the Licensed Rights, such
+     as reproduction, public display, public performance, distribution,
+     dissemination, communication, or importation, and to make material
+     available to the public including in ways that members of the
+     public may access the material from a place and at a time
+     individually chosen by them.
+
+  m. Sui Generis Database Rights means rights other than copyright
+     resulting from Directive 96/9/EC of the European Parliament and of
+     the Council of 11 March 1996 on the legal protection of databases,
+     as amended and/or succeeded, as well as other essentially
+     equivalent rights anywhere in the world.
+
+  n. You means the individual or entity exercising the Licensed Rights
+     under this Public License. Your has a corresponding meaning.
+
+=======================================================================
+
+Section 2 -- Scope.
+
+  a. License grant.
+
+       1. Subject to the terms and conditions of this Public License,
+          the Licensor hereby grants You a worldwide, royalty-free,
+          non-sublicensable, non-exclusive, irrevocable license to
+          exercise the Licensed Rights in the Licensed Material to:
+
+            a. reproduce and Share the Licensed Material, in whole or
+               in part; and
+
+            b. produce, reproduce, and Share Adapted Material.
+
+       2. Exceptions and Limitations. For the avoidance of doubt, where
+          Exceptions and Limitations apply to Your use, this Public
+          License does not apply, and You do not need to comply with
+          its terms and conditions.
+
+       3. Term. The term of this Public License is specified in Section
+          6(a).
+
+       4. Media and formats; technical modifications allowed. The
+          Licensor authorizes You to exercise the Licensed Rights in
+          all media and formats whether now known or hereafter created,
+          and to make technical modifications necessary to do so. The
+          Licensor waives and/or agrees not to assert any right or
+          authority to forbid You from making technical modifications
+          necessary to exercise the Licensed Rights, including
+          technical modifications necessary to circumvent Effective
+          Technological Measures. For purposes of this Public License,
+          simply making modifications authorized by this Section 2(a)
+          (4) never produces Adapted Material.
+
+       5. Downstream recipients.
+
+            a. Offer from the Licensor -- Licensed Material. Every
+               recipient of the Licensed Material automatically
+               receives an offer from the Licensor to exercise the
+               Licensed Rights under the terms and conditions of this
+               Public License.
+
+            b. Additional offer from the Licensor -- Adapted Material.
+               Every recipient of Adapted Material from You
+               automatically receives an offer from the Licensor to
+               exercise the Licensed Rights in the Adapted Material
+               under the conditions of the Adapter's License You apply.
+
+            c. No downstream restrictions. You may not offer or impose
+               any additional or different terms or conditions on, or
+               apply any Effective Technological Measures to, the
+               Licensed Material if doing so restricts exercise of the
+               Licensed Rights by any recipient of the Licensed
+               Material.
+
+       6. No endorsement. Nothing in this Public License constitutes
+          or may be construed as permission to assert or imply that You
+          are, or that Your use of the Licensed Material is, connected
+          with, or sponsored, endorsed, or granted official status by,
+          the Licensor or others designated to receive attribution as
+          provided in Section 3(a)(1)(A)(i).
+
+  b. Other rights.
+
+       1. Moral rights, such as the right of integrity, are not
+          licensed under this Public License, nor are publicity,
+          privacy, and/or other similar personality rights; however, to
+          the extent possible, the Licensor waives and/or agrees not to
+          assert any such rights held by the Licensor to the limited
+          extent necessary to allow You to exercise the Licensed
+          Rights, but not otherwise.
+
+       2. Patent and trademark rights are not licensed under this
+          Public License.
+
+       3. To the extent possible, the Licensor waives any right to
+          collect royalties from You for the exercise of the Licensed
+          Rights, whether directly or through a collecting society
+          under any voluntary or waivable statutory or compulsory
+          licensing scheme. In all other cases the Licensor expressly
+          reserves any right to collect such royalties.
+
+=======================================================================
+
+Section 3 -- License Conditions.
+
+Your exercise of the Licensed Rights is expressly made subject to the
+following conditions.
+
+  a. Attribution.
+
+       1. If You Share the Licensed Material (including in modified
+          form), You must:
+
+            a. retain the following if it is supplied by the Licensor
+               with the Licensed Material:
+
+                 i. identification of the creator(s) of the Licensed
+                    Material and any others designated to receive
+                    attribution, in any reasonable manner requested by
+                    the Licensor (including by pseudonym if
+                    designated);
+
+                ii. a copyright notice;
+
+               iii. a notice that refers to this Public License;
+
+                iv. a notice that refers to the disclaimer of
+                    warranties;
+
+                 v. a URI or hyperlink to the Licensed Material to the
+                    extent reasonably practicable;
+
+            b. indicate if You modified the Licensed Material and
+               retain an indication of any previous modifications; and
+
+            c. indicate the Licensed Material is licensed under this
+               Public License, and include the text of, or the URI or
+               hyperlink to, this Public License.
+
+       2. You may satisfy the conditions in Section 3(a)(1) in any
+          reasonable manner based on the medium, means, and context in
+          which You Share the Licensed Material. For example, it may be
+          reasonable to satisfy the conditions by providing a URI or
+          hyperlink to a resource that includes the required
+          information.
+
+       3. If requested by the Licensor, You must remove any of the
+          information required by Section 3(a)(1)(A) to the extent
+          reasonably practicable.
+
+=======================================================================
+
+Section 4 -- Sui Generis Database Rights.
+
+Where the Licensed Rights include Sui Generis Database Rights that
+apply to Your use of the Licensed Material:
+
+  a. for the avoidance of doubt, Section 2(a)(1) grants You the right
+     to extract, reuse, reproduce, and Share all or a substantial part
+     of the contents of the database;
+
+  b. if You include all or a substantial part of the database contents
+     in a database in which You have Sui Generis Database Rights, then
+     the database in which You have Sui Generis Database Rights (but
+     not its individual contents) is Adapted Material; and
+
+  c. You must comply with the conditions in Section 3(a) if You Share
+     all or a substantial part of the contents of the database.
+
+For the avoidance of doubt, this Section 4 supplements and does not
+replace Your obligations under this Public License where the Licensed
+Rights include other Copyright and Similar Rights.
+
+=======================================================================
+
+Section 5 -- Disclaimer of Warranties and Limitation of Liability.
+
+  a. UNLESS OTHERWISE SEPARATELY UNDERTAKEN BY THE LICENSOR, TO THE
+     EXTENT POSSIBLE, THE LICENSOR OFFERS THE LICENSED MATERIAL AS-IS
+     AND AS-AVAILABLE, AND MAKES NO REPRESENTATIONS OR WARRANTIES OF
+     ANY KIND, WHETHER EXPRESS, IMPLIED, STATUTORY, OR OTHER. THIS
+     INCLUDES, WITHOUT LIMITATION, WARRANTIES OF TITLE,
+     MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE,
+     NON-INFRINGEMENT, ABSENCE OF LATENT OR OTHER DEFECTS, ACCURACY, OR
+     THE PRESENCE OR ABSENCE OF ERRORS, WHETHER OR NOT KNOWN OR
+     DISCOVERABLE. WHERE DISCLAIMERS OF WARRANTIES ARE NOT ALLOWED IN
+     FULL OR IN PART, THIS DISCLAIMER MAY NOT APPLY TO YOU.
+
+  b. TO THE EXTENT POSSIBLE, IN NO EVENT WILL THE LICENSOR BE LIABLE
+     TO YOU ON ANY LEGAL THEORY (INCLUDING, WITHOUT LIMITATION,
+     NEGLIGENCE) OR OTHERWISE FOR ANY DIRECT, SPECIAL, INDIRECT,
+     INCIDENTAL, CONSEQUENTIAL, PUNITIVE, EXEMPLARY, OR OTHER LOSSES,
+     COSTS, EXPENSES, OR DAMAGES ARISING OUT OF THIS PUBLIC LICENSE OR
+     USE OF THE LICENSED MATERIAL, EVEN IF THE LICENSOR HAS BEEN
+     ADVISED OF THE POSSIBILITY OF SUCH LOSSES, COSTS, EXPENSES, OR
+     DAMAGES. WHERE A LIMITATION OF LIABILITY IS NOT ALLOWED IN FULL OR
+     IN PART, THIS LIMITATION MAY NOT APPLY TO YOU.
+
+  c. The disclaimer of warranties and limitation of liability provided
+     above shall be interpreted in a manner that, to the extent
+     possible, most closely approximates an absolute disclaimer and
+     waiver of all liability.
+
+=======================================================================
+
+Section 6 -- Term and Termination.
+
+  a. This Public License applies for the term of the Copyright and
+     Similar Rights licensed here. However, if You fail to comply with
+     this Public License, then Your rights under this Public License
+     terminate automatically.
+
+  b. Where Your right to use the Licensed Material has terminated under
+     Section 6(a), it reinstates:
+
+       1. automatically as of the date the violation is cured, provided
+          it is cured within 30 days of Your discovery of the
+          violation; or
+
+       2. upon express reinstatement by the Licensor.
+
+     For the avoidance of doubt, this Section 6(b) does not affect any
+     right the Licensor may have to seek remedies for Your violations
+     of this Public License.
+
+  c. For the avoidance of doubt, the Licensor may also offer the
+     Licensed Material under separate terms or conditions or stop
+     distributing the Licensed Material at any time; however, doing so
+     will not terminate this Public License.
+
+  d. Sections 1, 5, 6, 7, and 8 survive termination of this Public
+     License.
+
+=======================================================================
+
+Section 7 -- Other Terms and Conditions.
+
+  a. The Licensor shall not be bound by any additional or different
+     terms or conditions communicated by You unless expressly agreed.
+
+  b. Any arrangements, understandings, or agreements regarding the
+     Licensed Material not stated herein are separate from and
+     independent of the terms and conditions of this Public License.
+
+=======================================================================
+
+Section 8 -- Interpretation.
+
+  a. For the avoidance of doubt, this Public License does not, and
+     shall not be interpreted to, reduce, limit, restrict, or impose
+     conditions on any use of the Licensed Material that could lawfully
+     be made without permission under this Public License.
+
+  b. To the extent possible, if any provision of this Public License is
+     deemed unenforceable, it shall be automatically reformed to the
+     minimum extent necessary to make it enforceable. If the provision
+     cannot be reformed, it shall be severed from this Public License
+     without affecting the enforceability of the remaining terms and
+
+     conditions.
+
+  c. No term or condition of this Public License will be waived and no
+     failure to comply consented to unless expressly agreed to by the
+     Licensor.
+
+  d. Nothing in this Public License constitutes or may be interpreted
+     as a limitation upon, or waiver of, any privileges and immunities
+     that apply to the Licensor or You, including from the legal
+     processes of any jurisdiction or authority.
+
+=======================================================================
+
+Creative Commons is not a party to its public licenses. Notwithstanding,
+Creative Commons may elect to apply one of its public licenses to material
+it publishes and in those instances will be considered the "Licensor".
+The text of the Creative Commons public licenses is dedicated to the
+public domain under the CC0 Public Domain Dedication. Except for the
+limited purpose of indicating that material is shared under a Creative
+Commons public license or as otherwise permitted by the Creative Commons
+policies published at creativecommons.org/policies, Creative Commons
+does not authorize the use of the trademark "Creative Commons" or any
+other trademark or logo of Creative Commons without its prior written
+consent including, without limitation, in connection with any
+unauthorized modifications to any of its public licenses or any other
+arrangements, understandings, or agreements concerning use of licensed
+material. For the avoidance of doubt, this paragraph does not form part
+of the public licenses.
+
+Creative Commons may be contacted at creativecommons.org.
+

README.md

@@ -1,4 +1,27 @@
 ---
+pretty_name: SynthMT
+annotations_creators:
+- no-annotation
+language:
+- en
+license: cc-by-4.0
+tags:
+- microscopy
+- synthetic-data
+- microtubules
+- irm
+- tirf
+- biology
+- instance-segmentation
+- computer-vision
+- foundation-models
+- segmentation
+task_categories:
+- image-segmentation
+task_ids:
+- instance-segmentation
+size_categories:
+- around_10k
 dataset_info:
   features:
   - name: id
@@ -6,16 +29,158 @@ dataset_info:
   - name: image
     dtype: image
   - name: mask
-    list: image
+    dtype:
+      array3_d:
+        shape:
+        - null
+        - 512
+        - 512
+        dtype: uint16
   splits:
   - name: train
-    num_bytes: 3063820
-    num_examples: 5
-  download_size: 3049613
-  dataset_size: 3063820
+    num_bytes: 43191602168
+    num_examples: 6600
+  download_size: 3943294163
+  dataset_size: 43191602168
 configs:
 - config_name: default
   data_files:
   - split: train
     path: data/train-*
 ---
+
+
+# SynthMT: A Synthetic Benchmark for Automated Microtubule Segmentation
+
+**Authors:** Mario Koddenbrock*, Justus Westerhoff*, Dominik Fachet, Simone Reber, Felix Gers, Erik Rodner  
+**Affiliations:** HTW Berlin, BHT Berlin, MPI for Infection Biology  
+**Code & Pipeline:** https://github.com/ml-lab-htw/SynthMT  
+**Paper:** *Synthetic Data Enables Human-Grade Microtubule Analysis by Tuning Segmentation Foundation Models*  
+**Dataset:** https://huggingface.co/datasets/HTW-KI-Werkstatt/SynthMT
+
+
+_`*Equal contribution`_
+
+# 🧬 Overview
+
+**SynthMT** is a synthetic, expert-validated dataset designed to benchmark segmentation models on *in vitro* microtubule (MT) images recorded in interference reflection microscopy (IRM)–like conditions.  
+It provides:
+
+- Realistic **synthetic MT images**  
+- Pixel-perfect **instance segmentation labels**  
+- A **label-free generation pipeline** that adapts to any real microscope domain  
+- A comprehensive benchmark of **classical**, **microscopy-specialized**, and **general-purpose foundation models** (SAM, SAM2, SAM3, SAM3Text)
+
+A core result of the associated paper:  
+→ **SAM3Text**, prompted with *“thin line”* and tuned on **only 10 synthetic images**, achieves **near-human or super-human** segmentation accuracy on unseen real data.
+
+---
+
+# 🖼 Example from the Dataset (Figure 1)
+
+<div align="center">
+
+<table>
+<tr>
+<td align="center"><b>(a) IRM-like synthetic image</b><br><img src="assets/fig_1_image.png" width="95%"></td>
+<td align="center"><b>(b) Ground-truth instance mask</b><br><img src="assets/fig_1_gt.png" width="95%"></td>
+</tr>
+<tr>
+<td align="center"><b>(c) FIESTA anchor point predictions</b><br><img src="assets/fig_1_fiesta.png" width="95%"></td>
+<td align="center"><b>(d) SAM3Text segmentation</b><br><img src="assets/fig_1_sam3text.png" width="95%"></td>
+</tr>
+</table>
+
+**Figure 1 — Overview of SynthMT and example predictions.**
+
+</div>
+
+---
+
+# 📦 Dataset Structure
+
+Each sample in SynthMT contains:
+
+| Field | Type | Description |
+|---|---|---|
+| `id` | `string` | Image identifier |
+| `image` | `Image` | Synthetic IRM-like image, decoded from a PNG file. |
+| `mask` | `Array3D` | Instance-ID mask with shape (C, 512, 512) and `uint16` dtype. `C` is the number of channels (instances). `0` is background. |
+
+
+Masks use **instance IDs** rather than binary stacks.
+
+---
+
+# 🧫 Biological Motivation
+
+Microtubules (MTs) are cytoskeletal filaments essential for intracellular transport, cell motility, and mitotic spindle formation. Measuring MT **count**, **length**, and **curvature** is critical for *in vitro* reconstitution experiments, drug discovery, and mechanistic cell biology.
+
+However:
+
+- Manual MT annotation is time-consuming and unscalable  
+- IRM/TIRF imaging varies significantly across labs (domain shift)  
+- No large, labeled benchmarks existed for MT segmentation  
+
+**SynthMT** directly addresses this gap.
+
+---
+
+# 📥 Installation & Loading
+
+To load the dataset, first install the Hugging Face `datasets` library:
+
+```bash
+pip install datasets
+```
+
+Then, use the following Python code:
+
+```python
+from datasets import load_dataset
+
+ds = load_dataset("HTW-KI-Werkstatt/SynthMT")
+
+sample = ds["train"][0]
+sample["image"].show()
+sample["mask"].show()
+````
+
+---
+
+# 🔗 Links
+
+* **Dataset:** [https://huggingface.co/datasets/HTW-KI-Werkstatt/SynthMT](https://huggingface.co/datasets/HTW-KI-Werkstatt/SynthMT)
+* **Code & Generation Pipeline:** [https://github.com/ml-lab-htw/SynthMT](https://github.com/ml-lab-htw/SynthMT)
+* **Paper:** available soon
+
+---
+
+# 📄 Citation
+
+If you use SynthMT, please cite:
+
+```bibtex
+@article{tba,
+  title={TBA},
+  author={TBA},
+  journal={arXiv},
+  year={2026}
+}
+```
+
+---
+
+# 🏷 License
+
+**CC-BY-4.0** - See [LICENSE](LICENSE) for details.
+
+---
+
+# 🙏 Acknowledgements
+
+We thank the researchers and microscopy experts involved in evaluating the perceptual realism and biological plausibility of SynthMT.
+
+---
+
+