MacNeil, Liam; Joly, Léa J; Ito, Maysa; Steinmann, Anna; Drakula, Maja; Wiegand, Hannes; Morsbach, Samuel; Karnatz, Josefine; Scotti, Marco (2024): Hydrobiid mudsnail image dataset: Raw stereomicroscope, processed, and segmented images of abundant brackish snails from a mesocosm experiment with multiple temperature treatments [dataset]. PANGAEA, https://doi.org/10.1594/PANGAEA.957929
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Abstract:
We examined the growth response of a brackish snail (Hydrobiidae) against multiple temperature treatments in a mesocosm located beside the Alfred Wegener Institute Wadden Sea Station on Sylt (55°01′19.2″N, 8°26′17.7″E). Bulk sediments were collected south of Pellworm (54° 31' 55.83"N, 8° 42' 40.36"E) at low tide on March 22, 2022, transferred to mesh-lined crates and introduced to mesocosm tanks (170 cm × 85 cm × 1800 L). Experimental warming treatments were conducted using three heaters per tank (Titanium heater 500 W, Aqua Medic, Bissendorf, Germany). The full specifications for the mesocosms are already published (Pansch et al., 2016). Throughout the experimental warming period, four sampling events (March 30, April 25, May 24, June 20) were conducted to core sediments. Sediment cores were washed and sieved (1mm mesh size) to disaggregate infauna. Individuals were separated for the common hydrobiid mudsnail, which were subsequently imaged in groups on a typical petri plate under stereomicroscopy. A semi-automatic object segmentation and size measurement approach was developed to rapidly differentiate and measure individuals from images. Segmentation was highly accurate and precise against manual length measurements (end-to-end; mm) collected in ImageJ for 4595 snails. Scaling the segmentation method across the full dataset estimated >40,000 snails and presented a complex species-specific response to warming. The enclosed dataset represents all raw, processed, and segmented images (n= 3201) produced by this study.
Keyword(s):
Supplement to:
MacNeil, Liam; Joly, Léa J; Ito, Maysa; Steinmann, Anna; Mehler, Knut; Scotti, Marco (accepted): Sizing mudsnails: Applying superpixels to scale growth detection under ocean warming. Methods in Ecology and Evolution
References:
Pansch, Andreas; Winde, Vera; Asmus, Ragnhild; Asmus, Harald (2016): Tidal benthic mesocosms simulating future climate change scenarios in the field of marine ecology. Limnology and Oceanography-Methods, 14(4), 257-267, https://doi.org/10.1002/lom3.10086
Project(s):
Funding:
Federal Ministry of Education and Research (BMBF), grant/award no. 03F0913B: DAM sustainMare - iSeal, GEOMAR
Coverage:
Latitude: 55.022000 * Longitude: 8.438250
Date/Time Start: 2022-03-30T00:00:00 * Date/Time End: 2022-06-20T00:00:00
Event(s):
Sylt_Mesocosm_2022 * Latitude: 55.022000 * Longitude: 8.438250 * Date/Time Start: 2022-03-30T00:00:00 * Date/Time End: 2022-06-20T00:00:00 * Method/Device: Mesocosm experiment (MESO)
Comment:
3201 .tif files (2880 x 2048 px, RGB, 96 DPI). Equal number of raw, processed, and segmented files. The naming convention follows: Species_Sample_Treatment_Event_Tank_ImageNumber_Type.tif
Parameter(s):
| # | Name | Short Name | Unit | Principal Investigator | Method/Device | Comment |
|---|---|---|---|---|---|---|
| 1 | Type of study | Study type | MacNeil, Liam | |||
| 2 | Taxon/taxa, unique identification | Taxa UID | MacNeil, Liam | |||
| 3 | Taxon/taxa, unique identification (Semantic URI) | Taxa UID (Semantic URI) | MacNeil, Liam | |||
| 4 | Taxon/taxa, unique identification (URI) | Taxa UID (URI) | MacNeil, Liam | |||
| 5 | Sample code/label | Sample label | MacNeil, Liam | |||
| 6 | Treatment: temperature description | T:Temp descr | MacNeil, Liam | "amb" = Ambient seawater temperature; "1p5" = +1.5 degrees celcius above ambience; "three" = +3.0 degrees celcius above ambience | ||
| 7 | Sampling date/time, experiment | Date/time sampling exp | MacNeil, Liam | |||
| 8 | Identification | ID | MacNeil, Liam | Event ID related to sampling date | ||
| 9 | Tank number | Tank No | MacNeil, Liam | |||
| 10 | Image number/name | Image no/name | MacNeil, Liam | |||
| 11 | Type | Type | MacNeil, Liam | |||
| 12 | File type | File type | MacNeil, Liam | Extension | ||
| 13 | Method comment | Method comm | MacNeil, Liam | Mode | ||
| 14 | Resolution | Resolution | MacNeil, Liam | |||
| 15 | Magnification | Mag | MacNeil, Liam | |||
| 16 | Image, specimens | IMAGE spec | MacNeil, Liam | Stereo microscope, Nikon, SMZ18; coupled with Microscope camera, Nikon, DS-Fi3 [5.39 megapixels, LED base light with oblique coherent contrast] | ||
| 17 | Image, specimens (Media Type) | IMAGE spec (Type) | MacNeil, Liam | Stereo microscope, Nikon, SMZ18; coupled with Microscope camera, Nikon, DS-Fi3 [5.39 megapixels, LED base light with oblique coherent contrast] | ||
| 18 | Image, specimens (File Size) | IMAGE spec (Size) | Bytes | MacNeil, Liam | Stereo microscope, Nikon, SMZ18; coupled with Microscope camera, Nikon, DS-Fi3 [5.39 megapixels, LED base light with oblique coherent contrast] | |
| 19 | Image, specimens (MD5 Hash) | IMAGE spec (Hash) | MacNeil, Liam | Stereo microscope, Nikon, SMZ18; coupled with Microscope camera, Nikon, DS-Fi3 [5.39 megapixels, LED base light with oblique coherent contrast] |
License:
Creative Commons Attribution 4.0 International (CC-BY-4.0)
Status:
Curation Level: Enhanced curation (CurationLevelC)
Size:
44814 data points
Download Data
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