Quantitative Imaging Platform of Villefranche sur mer
piqv@imev-mer.fr
VERSION 8.26 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 8.26 deals with both locations of the Vuescan application
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.
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.
What is the PIQv ?
The Quantitative Imaging Platform (PIQv) is part of the Institut de la Mer de Villefranche sur mer (IMEV). The platform is also part of EMBRC France and labelled GIS IBISA via the MICCA platform.
The PIQv was created by engeeners and researchers from Laboratoire d’Océanographie de Villefranche-sur-Mer (LOV) and keeps being piloted by the COMPLEx team of LOV.
The platform employs taxonomists and instrument/software specialists to offer the best quality of services using laboratory and underwater imaging instrument and software.
The PIQv runs tools permitting to characterize and identify objects/organisms from 20µm to few cm (FlowCam, Zooscan, UVP5 and UVP6). It will soon host the IFCB imaging system permitting to lower the size down to few µm.
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).
