STL10-Labeled

This public repo contains labels for the unlabeled pictures in the stl10 dataset. Please refer to files Files and versions tab above. You can also refer to my original repo https://github.com/semihyagli/STL10-Labeled Please consider sponsoring this repo so that we can continue to develop high-quality datasets for the ML/AI research. To become a sponsor: GitHub Sponsors Buy me a coffee You can also sponsor us by downloading our free application, Etiqueta, to your… See the full description on the dataset page: https://huggingface.co/datasets/semihyagli/STL10-Labeled.

STL10 - Segmentation

Please consider sponsoring this repo so that we can continue to develop high-quality datasets for the AI and ML research. To become a sponsor: GitHub Sponsors Buy me a coffee You can also sponsor us by downloading our free application, Etiqueta, to your devices: Etiqueta on iOS or Apple Chip Macs Etiqueta on Android This repo contains segmented images for the labeled part of the STL-10 Dataset.
If you are looking for STL10-Labeled variant of the dataset… See the full description on the dataset page: https://huggingface.co/datasets/semihyagli/STL10-Segmented.

The current data set refers to the study of fossil fish material from Southwest Ireland (Placodermi, Antiarchi; Givetian of the Iveragh Peninsula). The data consist of SEM elemental mapping (section 1), CTscan image stacks and subsequent working files (i.e. segmentation, visualisation files, STLs and 3D PDF files; sections 2-5), as well as phylogenetic analyses related to the genus Bothriolepis studied in the article (section 6). * Zoobank LSID for article: urn:lsid:zoobank.org:pub:0438B3D4-AEAA-4000-A1CB-B5DA0ECA466F * Zoobank LSID for taxon Bothriolepis dairbhrensis: urn:lsid:zoobank.org:act:B577F075-1EF6-48A5-8C7C-E64E36E2BC4E

The dataset corresponding to the article

Dupret, Byrne, Castro, Hammer, Higgs, Long, Niedźwiedzki, Qvarnström, Stössel & Ahlberg. In Press. The Bothriolepis (Placodermi, Antiarcha) material from the Valentia Slate Formation of the Iveragh Peninsula (middle Givetian, Ireland): morphology, evolutionary and systematic considerations, phylogenetic and palaeogeographic implications. PLOS ONE. with the LSID urn:lsid:zoobank.org:pub:0438B3D4-AEAA-4000-A1CB-B5DA0ECA466F and the species Bothriolepis dairbhrensis Dupret, Byrne, Castro, Hammer, Higgs, Long, Gzegorz Niedźwiedzki, Qvarnström, Stössel & Ahlberg with the LSID urn:lsid:zoobank.org:act:B577F075-1EF6-48A5-8C7C-E64E36E2BC4E

is composed of the following files:

1. Elemental analysis (SEM) equipment: Hitachi S–3600N Scanning Electron Microscope (SEM); JPGS are original output.

2. CT-scans datasets In London, the material was CT-scanned with a Nikon HMX ST 225 system, Nikon Metrology, Leuven, Belgium, with a tungsten reflection target. Detailed settings files were adjusted for each specimen and are given in associated documentation "S2 Table-scan properties.xlsx". Two specimens required stitching performed with an in-house NHM script written in Octave. In Oslo, the scanning was carried out with a Nikon Metrology XT H 225 ST microfocus CT instrument at the Natural History Museum, University of Oslo, at 160-220 kV, 1 s exposure time, 3016 projections, and with tin filters of varying thickness. Voxel resolution was 75 µm or better. Detailed settings are given in in associated documentation "S2 Table-scan properties.xlsx".

3. Drishti and Mimics files (segmentation)

4. STL files

5. 3D pdfs In Mimics, each individual structure corresponding to a mask was used to generate a high quality 3D object, itself transformed into an STL file. Each 3D object was duplicated and relocated in the 3D space; once again STLs were generated. The STL files were then imported into Materialise 3-matic (v. 15.0) and were reorganised into anatomical ensembles (head, fin, etc.) in both original and correct positions. Each STL surface was then simplified and corrected using the following functions: Filter Sharp Triangles with filter distance 0.01; Filter Small Edges with filter distance 0.01; Improve Mesh with shape quality high/medium, maximum geometrical error 0.07, and maximal edge length 20.0. A 3D pdf file was finally generated and open in Adobe Acrobat to take pictures used in figures of the current article.

for the following specimens a. NMING:F35203-UU210ab_HQ Bothriolepis dairbhrensis sp. nov. Incomplete lateral plate and fragment of indeterminate plate. Segmentation in Mimics, treatment of STLS and 3d PDF exportation in 3-matic. The scale of the reference cube edges is 10 mm. Please note that within the Mimics project files for this specimen µm is incorrectly given as a base of measurement when it should be mm (millimeters). All other processing has been performed treating the source data as being scaled in millimeters.

b. NMING:F35229-CH003 Bothriolepis dairbhrensis sp. nov. Assemblage of indeterminate plate and indeterminate scavenging gastropods. Segmentation in Mimics, treatment of STLS and 3d PDF exportation in 3-matic. The scale of the reference cube edges is 10 mm.

c. NMING:F35216-UU SFB001 Bothriolepis dairbhrensis sp. nov. Proximal segment of the pectoral fin, with AVL and articular condyle. [ORG] corresponds to plates in original position; [RELOC] corresponds to plates relocated in life position. Segmentation in Mimics, treatment of STLS and 3d PDF exportation in 3-matic. The scale of the reference cube edges is 10 mm.

d. NHM P 59677 (complete, ORG end RELOC files) Bothriolepis dairbhrensis sp. nov. Incomplete head (and endocranial processes), ventral body armour and proximal segment of the pectoral fin. [ORG] corresponds to plates in original position; [RELOC] corresponds to plates relocated in life position. Segmentation in Mimics, treatment of STLS and 3d PDF exportation in 3-matic. The scale of the reference cube edges is 10 mm.

e. NHM P 59678 Bothriolepis dairbhrensis sp. nov. Incomplete lateral and indeterminate plates of an adult individual. The scale of the reference cube edges is 10 mm.

f. NHM P 59679 Bothriolepis dairbhrensis sp. nov. Two indeterminate fragments. The scale of the reference cube edges is 10 mm.

g. NHM P 59687 Bothriolepis dairbhrensis sp. nov. Indeterminate fragments and burrows. The scale of the reference cube edges is 10 mm.

1. taxon*character matrices with different sets of analyses (readible in MESQUITE)

LINKS TO PREVIOUSLY MENTIONED SOLUTIONS MESQUITE (construction of data matrix, visualisation): https://www.mesquiteproject.org/ https://github.com/MesquiteProject/ Maddison, W. P. and D.R. Maddison. 2021. Mesquite: a modular system for evolutionary analysis. Version 3.70 http://www.mesquiteproject.org

ZEPHYR (Mesquite package for interacting with external phylogeny inference programs) http://zephyr.mesquiteproject.org/ Maddison, D.R., & W.P. Maddison. 2021. Zephyr: a Mesquite package for interacting with external phylogeny inference programs. Version 3.20. http://zephyr.mesquiteproject.org

TNT (phylogenetic analysis) https://onlinelibrary.wiley.com/doi/10.1111/j.1096-0031.2008.00217.x Goloboff, P.A., Farris, J.S. and Nixon, K.C. (2008), TNT, a free program for phylogenetic analysis. Cladistics, 24: 774-786. https://doi.org/10.1111/j.1096-0031.2008.00217.x

MATERIALISE MIMICS and 3-MATIC (segmentation, 3D modelling): https://www.materialise.com/en/healthcare/mimics-innovation-suite

DRISHTI (3D visualisation): https://github.com/nci/drishti Ajay Limaye; Drishti: a volume exploration and presentation tool. Proc. SPIE 8506, Developments in X-Ray Tomography VIII, 85060X (October 17, 2012)