Embedded Files
ZQC : A NEW TOOL TO CHECK THE QUALITY OF ZOOSCAN ANALYSIS !
The Quantitative Imaging Platform (PIQv) is part of the Marine Institute of Villefranche-sur-Mer (IMEV). It is a component of the Microscopy and Imaging Platform of the French Riviera (MICA), certified by IBiSA. Accessible to all IMEV staff.
The PIQv is also open to external users (public or private sectors) through the EMBRC-France, which provides access to ecosystems, marine biological resources, state-of-the-art equipment, and complementary expertise from the three marine stations of Sorbonne University and CNRS: Banyuls, Roscoff, and Villefranche-sur-Mer.
The platform employs taxonomists and instrument/software specialists to provide high-quality services using laboratory and underwater imaging instruments and software.
The PIQv operates tools that allow for the characterization and identification of objects and organisms ranging from 20 µm to several centimeters (FlowCam, Zooscan, UVP5, and UVP6). It will soon host the IFCB imaging system, which will enable the detection of objects as small as a few µm.
VERSION 8.28 of ZOOPROCESS to download !
WARNING for Zooscan users who are experiencing Vuescan license problems
Vuescan must now be installed in Program Files. Check with Hydroptic if you need assistance. The new Zooprocess 8.27 deals with both locations of the Vuescan application
WARNING for Flowcam users who already imported their vignettes in EcoTaxa
The "recent" versions ( > 8.18) of Zooprocess permit to better compute the concentrations of the objects in the samples using new metadata issued from the summary files. If you did use a former version of Zooprocess to process your data, this warning does not apply.
We discovered a mistake in the computing of these concentration related fields in the TSV files for EcoTaxa. This error impacts the results as the the original total imaged volume was rounded instead of keeping its original precision. There is no way to be sure that your TSV is correct unless computed using version > 8.29 of Zooprocess. In order to correct your projects, Zooprocess 8.29 offers two new rapid functions that work in batch on a project and we recommend you to run them.
The recommended steps that can be applied to get exact values in EcoTaxa :
Update Zooprocess to version >= 8.29
Run the "Reconstruct all the PID & TSV files from the measurement files" tool (in the advanced menu)
Run the Correct the processed volumes in all the TSV files using the summary files (in the advanced menu)
Re-import the metadata of the project in EcoTaxa using the "Start re-import TSV files to update the metadata and data" tool
Re-export the results from your project to get the exact values allowing you to compute the exact abundances (which should not be very different from the previous ones)
Note : Zooprocess will create backup copies of the modified files in along with the corrected ones.
WARNING for Flowcam users who processed the raw images with Zooprocess
The Zooscan versions before 8.25 have been utilized to process B&W and RGB raw images and get the vignettes and ecotaxa*.tsv file for importation into EcoTaxa. We recently discovered that the object angle measurements were only 0 or 90 for the B&W datasets and thus suspected that other measurements were also wrong. The conclusion was that YES, all the measurements except the area were based on the overall vignette (excluding the footer) instead of the object pixels. We thus developed and tested the new Zooprocess 8.25 which both fixes the processing bug and allows you to use the vignettes to reprocess the measurements.
There are two options for obtaining correct measurements from existing datasets. The options depend on the status of the vignettes in EcoTaxa if they have already been imported:
the vignettes are either not imported or not validated,
the vignettes have already been imported and validated.
Check the Zooprocess download page for more information.
Read the HOW TO reprocess B&W Flowcam features procedure
WARNING for UVP6 users
The UVP6 data processed since 2023/11/12 with UVPapp 2.3 and imported in EcoPART and EcoTAXA have slightly wrong positions. We corrected (2024/02/20) the bug in EcoPART. It is recommended to re-load your data in EcoPART to get correct positions for the profiles/samples.
2024/01/12 WARNING on EcoTAXA trainings
The EcoTAXA application is currently undergoing improvements, with most pages being recently updated. However, we are currently facing limitations in human resources and, as a priority, have decided to enhance the online documentation of the application. Regrettably, this means we have to cancel the scheduled EcoTAXA trainings, and we sincerely apologize for any inconvenience caused. Please accept our apologies.
Plankton was sampled with various nets, from bottom or 500m depth to the surface, in many oceans of the world. Samples were imaged with a ZooScan. The full images were processed with ZooProcess which generated regions of interest (ROIs) around each individual object and a set of associated features measured on the object (see Gorsky et al 2010 for more information). The same objects were re-processed to compute features with the scikit-image toolbox (http://scikit-image.org). The 1,433,278 resulting objects were sorted by a limited number of operators, following a common taxonomic guide, into 93 taxa, using the web application EcoTaxa (http://ecotaxa.obs-vlfr.fr).
Quantitative Imaging Platform of Villefranche sur MerStation Zoologique 181 chemin du Lazaret06230 Villefranche sur Mer - France
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