Jan SchulzJade University of Applied Sciences · Department of Engineering Sciences
Jan Schulz
Dr. rer. nat.
About
73
Publications
21,746
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600
Citations
Citations since 2017
Introduction
Additional affiliations
June 2011 - February 2022
Position
- Senior Researcher
Description
- Senior scientist; Marine optics; Data analysis; Study course 'Marine Sensors'
March 2009 - June 2011
IMARE Institut für Marine Ressourcen GmbH
Position
- Vice section head
Description
- Vice section head
October 2002 - March 2009
Publications
Publications (73)
(English abstract below)
Kurzfassung
Optische Technologien und Verfahren sind sowohl in der limnischen als auch marinen Forschung Deutschlands über alle Bereiche und Skalen etabliert und entwickeln sich rasant weiter. Die Arbeitsgruppe „Aquatische Optische Technologien“ (AOT) will Forschern und Anwendern eine Plattform bieten, die Wissenstransfer...
In situ imaging of small particles and biota in the water column is commonly used by scientists. Scrutinising such objects by imaging confronts system designers and researchers with a number of technical challenges. Here physical and technical aspects of optical subsea technologies are discussed, including parameters for the identifi cation of suit...
In diesem Artikel wird die funktionale Ähnlichkeitssuche technischer Bauteile behandelt. Ziel ist es, ein Verfahren aufzuzeigen, welches eine Ähnlichkeitssuche innerhalb einer bionischen 3D-Datenbank mit verschiedensten Strukturen ermöglicht, ohne direkt auf die Geometriedaten der einzelnen Strukturen zurückzugreifen. Vielmehr werden mechanische Fu...
The deep basins in the Baltic Sea such as the Bornholm Basin (BB) are subject to seasonal changes in the strength of physico-chemical stratification. These depth-related changes in key abiotic factors are strong drivers of habitat partitioning by the autochthonous zooplankton community. Species-specific ecophysiological preferences often result in...
Zooplankton is a key element in aquatic food webs. Rapid mapping of
abundance, combined with information on taxonomic and size composition
is necessary to understand ecosystem dynamics. Classical sampling with
towed plankton nets does not allow resolving fine scale distributions
along hydrographic gradients (e.g. fronts and clines) although such
st...
https://www.jade-hs.de/en/unsere-hochschule/fachbereiche/ingenieurwissenschaften/studiengaenge/meerestechnik/
Coastal observatories are key to improve the understanding of processes within the coastal area and their interactions with regional and global environmental changes. The land-sea transition zone is an essential area that allows research on unique scientific questions under anthropogenic and natural influences. Amid the Wadden Sea UNESCO world natu...
Rapid changes of the biosphere observed in recent years are caused by both small and large scale drivers, like shifts in temperature, transformations in land-use, or changes in the energy budget of systems. While the latter processes are easily quantifiable, documentation of the loss of biodiversity and community structure is more difficult. Change...
In this paper we review the technologies available to make globally quantitative observations of particles in general-and plankton in particular-in the world oceans, and for sizes varying from sub-microns to centimeters. Some of these technologies have been available for years while others have only recently emerged. Use of these technologies is cr...
Images taken by LOKI on transects along 61°S and 3°13´ S off Peru during RV METEOR cruise 77/4 between February 2 and 4, 2009. See also Hirche et al.2014, High resolution vertical distribution of the copepod Calanus chilensis in relation to the shallow oxygen minimum zone off northern Peru. Deep-Sea Research I 88, 63-73
Marine optical imaging has become a major assessment tool in science, policy and public understanding of our seas and oceans. Methodology in this field is developing rapidly, including hardware, software and the ways of their application. The aim of the Marine Imaging Workshop (MIW) is to bring together academics, research scientists and engineers,...
The Coastal Observing System for Northern and Arctic Seas (COSYNA) was established in order to better understand the complex interdisciplinary processes of northern seas and the Arctic coasts in a changing environment. Particular focus is given to the German Bight in the North Sea as a prime example of a heavily used coastal area, and Svalbard as a...
In this work we are presenting an imaging hardware and post-processing analysis method for geo-morphological investigation of the transition zone between open sea and shore by inexpensive manned airborne systems. Aerial pictures are analysed for surface water wave characteristics and segmented for different ground substrates.
During an expedition with RV Heincke in October 2014 five stations in the Norwegian Sognefjord were sampled using the Lightframe On-sight Keyspecies Investigation system (LOKI, Schulz et al. 2010). This in-situ optical sampling device allows assigning ambient environmental parameters with simultaneously taken high quality images on scales of a few...
This paper shows the use of a specific type of time series analyses, the so named recurrence plot (RP), for investigations of the outer hull of an imaged and pre-segmented object to derive image features suitable for usage in classificators. Additionally to the features derived by the well documented recurrence quantification analysis (RQA) a new s...
The Coastal Observing System for Northern and Arctic Seas (COSYNA) was established in order to better understand the complex interdisciplinary processes of northern seas and the arctic coasts in a changing environment. Particular focus is given to the German Bight in the North Sea as a prime example for a heavily used coastal area, and Svalbard as...
Claims:
Reflector emitter which generates a beam which is directed in the main emission direction with
• a combined reflector comprised of
• two or more mirror-coated rotational ellipsoid and being formed by an ellipsoid of rotation which is cut in a longitudinal plane running through both focal points and in a cross-sectional plane perpendicular t...
Optische Technologien und Verfahren sind sowohl in der limnischen als auch marinen Forschung Deutschlands über alle Bereiche und Skalen etabliert und entwickeln sich rasant weiter. Die Arbeitsgruppe „Aquatische Optische Technologien“ (AOT) will Forschern und Anwendern eine Plattform bieten, die Wissenstransfer fördert, der nationalen Entwicklergeme...
An in-situ plankton detection sensor for parallel sensing of biota and ambient environmental parameters for a moored station is presented. Such systems allow investigating biological processes in relation to physical parameters on short time scales.
Der bekannte Reflektorstrahler bündelt Strahlen von mehreren schwächeren Strahlungsquellen über verspiegelte Rotationsellipsoidenabschnitte und einen zentralen Hohlspiegel, die mit ihren Brennpunkten zusammenfallen, zu einem gemeinsamen starken Strahl. Dabei werden auftretende Randstrahlen nicht optimal ausgenutzt. Eine Effizienzsteigerung wird bei...
We present an empirical quality control protocol for above-water radiometric sampling focussing on identifying sunglint situations. Using hyperspectral radiometers, measurements were taken on an automated and unmanned seaborne platform in northwest European shelf seas. In parallel, a camera system was used to capture sea surface and sky images of t...
A modular optical system for the study of zooplankton is presented. Three device versions are available equipped with a high resolution camera and connecting facilities for a wide range of sensors: LOKI is a research platform combining a plankton net with a high resolution in-situ imaging system for recording vertical profiles of zooplankton distri...
Es ist eine Reflektorleuchte mit einem kombinierten Reflektor aus einem Rotationsellipsoidenabschnitt und einem weiteren Hohlspiegel mit Apertur bekannt. Dessen Mittelpunkt fällt mit dem ersten und der Aperturmittelpunkt mit dem zweiten Brennpunkt des Rotationsellipsoiden zusammen; die Lichtquelle ist im ersten Brennpunkt angeordnet. Diese Bauweise...
A reflector emitter includes a combination reflector having at least one elliptical concave mirror shaped as an ellipsoid of revolution section having first and second focal points disposed outside and inside of the ellipsoid of revolution section, respectively. The reflector emitter includes at least one light source at the second focal point. The...
In September 2005 the mesozooplankton distribution, taxonomic composition and community structure were studied on four cross-shelf and one coastal transects in the Spermonde Archipelago off Makassar (SW Sulawesi). A total of 47 higher taxonomic groups and 89 calanoid copepod species were identified. Copepods outnumbered the other mesozooplankton ta...
Bubble detection and quantification is of high relevance for the
observation of gas and fluid seeps within the marine environment. The
presented work suggests and successfully investigates the application of
an image processing strategy based on the optical flow concept followed
by a customised thresholding and a new segmentation approach. Both are...
In this short note we give an overview on the development of a new versatile plankton video recording system named LOKI. In addition to the introduction of technical specifications and background information of the device we also demonstrate a possible scientific application in a case study performed in an upwelling area off the Namibian coast.
The international Global Ocean Ecosystem Dynamics (GLOBEC) programme was initiated in 1991 by the Scientific Committee on Oceanic Research (SCOR) and the Intergovernmental Oceanographic Commission (IOC) of the UNESCO. It was a core project of the International Geosphere-Biosphere Project (IGBP) with its research topics aiming at understanding how g...
Die Erfindung bezieht sich auf eine Vorrichtung zur Partikeldetektion in einem strömenden Fluid in einem optisch begrenzten Messvolumen mit einer Beleuchtungseinrichtung aus einer Lichtquelle, einem Blendensystem und einem fokussierenden Linsensystem sowie mit einer optischen Auswerteinheit mit weiteren Blenden und Linsen und einem auf das Messvolu...
The Baltic Sea is the largest brackish water area of the world. On the basis of the data from 16 cruises, we show the seasonal and vertical distribution patterns of the appendicularians Fritillaria borealis, Oikopleura dioica and the cyclopoid copepod Oithona similis, in the highly stratified Bornholm Basin. These species live at least temporarily...
The vertical zonation of zooplankton in a deep central Baltic Sea basin was studied in relation to hydrography based on vertically resolved sampling. The study period covered different seasonal hydrographic conditions as well as inflow events of water masses from the North Sea, important for the physical condition of this marginal sea. By means of...
The Baltic Sea is the largest semi-enclosed brackish sea in the world and consists of several consecutive deep basins. Due to fresh water input, physical processes and topographic structures pronounced hydrographic stratifications persist. These are created from water masses of incompatible densities due to different temperatures and salinities.A t...
The Baltic Sea is the largest brackish water area of the world. On the basis of the data from 16 cruises, we show the seasonal and vertical distribution patterns of the appendicularians Fritillaria borealis, Oikopleura dioica and the cyclopoid copepod Oithona similis, in the highly stratified Bornholm Basin. These species live at least temporarily...
Vertical distribution of zooplankton species is controlled by physical parameters and thus affects predator-prey relationships and hence trophic interactions. Fish and gelatinous plankton often feed in distinct layers or show feeding migrations. Both temporal and spatial match are required for successful predation. Here we present data on the seaso...
Ziel der vorliegenden Arbeit war es, die Verteilung der beiden calciumbindenden Proteine CalbindinD28k (CB) und Calretinin (CR) in der afferenten Gehörbahn von Gallus gallus f. domestica aufzudecken. Zu diesem Zweck wurden von 14 Tieren des Alters P0 bis P40 die Innenohren als ‚whole mount‘ sowie Dünnschnitte des Gehirns immunhistochemisch nach der...
Questions
Questions (2)
I am trying to run some statistics on the contour outline of imaged zooplankton specimens from the LOKI system (https://www.researchgate.net/publication/236931182_Imaging_of_plankton_specimens_with_the_lightframe_on-sight_keyspecies_investigation_LOKI_system ).
The LOKI system extracts Regions Of Interest (ROI) directly in the underwater unit. Thus, each file generally contains the image of an individual specimen. It can be generally assumed, that the largest object in the image is the ROI to evaluate.
To get the contour information I use some functions of the EBImage package (see some sample code below). This works fine for most images.
Nevertheless, in some images the background is heterogeneous and a little brighter. Thus, the background may partially contribute as “false positive” to the ROI. In other cases parts of the background become structures of their own, being sometimes even larger than the ROI (see the two upper rows of the attached panel imge).
I already tried a couple of things like Otsu’s thresholding method or the filter2 functions. I also tried to first subtract a certain value and finally spread the range (multiplication or power function). So far I was not able to find a universal and simple approach.
The ROI is generally part of the brightest structures in the image. But specimen appendages may vary in brightness and be even close to the background. As these structures are also important the background cannot be simply darkened, as it would also loose some of these structures (see last row of the panel image).
Thus, an interesting approach might be to start from the brightest structures and to identify pixels above a local, adaptive threshold; something like a modified Hoshen-Koppelman algorithm.
Now is my question, whether here is someone who may give a hint, an approach or even some lines of code.
As I finally want to process >100k images it is of course advantageous to keep the solution as (computational) cheap as possible. However, to have a good solution is the preference.
Below I attached some quick code to get an idea.
Also included are some images for testing…
Best regards,
Jan
# short test on selected contour outlines of zooplankton specimens
# Dr. Jan Schulz, ICBM, University of Oldenburg
# data retrieved from a LOKI device (DOI: 10.2971/jeos.2010.10017s)
# file date: 30.09.2019
library ("EBImage")
#-------------------------------------------------------------------------------
# create a small fake matrix easily to distinguish from real images
# and to ensure proper functionality when an images could not be loaded correctly
# in subsequent image processing it will be used to emulate a smal 7*7 pixel image,
# with black background and a 3*3 pixels white dot in its centre
fakeMatrix = matrix (0, nrow = 7, ncol = 7)
fakeMatrix [3:5, 3:5] = 1
# initialise the greyIMG matrix with the tiny fake matrix
# just for security reasons, when import fails the routines calculate a very small
# image that can be identified pretty easily
greyIMG = fakeMatrix
aFileList = list ( "D:/Daten/HE434Test/0067_HE 434-067/Haul 1/LOKI_10001.01/Pictures/2014.10.20 11 25/20141020 112511 943 000000 2037 0102.png",
"D:/Daten/HE434Test/0067_HE 434-067/Haul 1/LOKI_10001.01/Pictures/2014.10.20 11 24/20141020 112403 993 000000 2073 0456.bmp",
"D:/Daten/HE434Test/0067_HE 434-067/Haul 1/LOKI_10001.01/Pictures/2014.10.20 11 24/20141020 112434 218 000000 0108 0933.bmp")
# create a file for the plot output
png (paste ("D:/Daten/HE434Test/0067_HE 434-067/Haul 1/Test", ".png"),
width = 21,
height = 29.7,
units = 'cm',
res = 310)
par (mfrow = c (3, 2), # display different plots as an 3x2 array
oma = c (4, 2, 3, 2), # define outer margins as lines of text
mar = c (5, 4, 2, 2))
for (i in 1:length (aFileList)) {
aFileFullPath = aFileList [[i]] [1]
# handle BMP images
if (toupper (tools::file_ext (aFileFullPath)) == "BMP")
{
#read the BMP image
aSourceImage = read.bmp (aFileFullPath)
# use the number of colour in the attributes to re-scale values to [0..1]
aSourceImage = aSourceImage [ , ] / max (attr (aSourceImage, "header")$ncolors)
greyIMG = channel (aSourceImage, "luminance")
}
#handle PNG images
if (toupper (tools::file_ext (aFileFullPath)) == "PNG")
{
# read the PNG file
aSourceImage = readPNG (aFileFullPath)
aSourceImage = channel (aSourceImage, "luminance")
greyIMG = aSourceImage [ , , 1]
}
#-------------------------- improve image and create a binary silhouette image
# do some image enhancing
# adding a value -> increase brightness
# multiplication -> increasing contrast
# power -> gamma correction
# greater as -> filter for pixels being bright enough
if (toupper (tools::file_ext (aFileFullPath)) == "BMP")
{
#enhancedgreyIMG = greyIMG [ , ] ^ 0.8
enhancedgreyIMG = (greyIMG [ , ]- min (greyIMG))*8
}
if (toupper (tools::file_ext (aFileFullPath)) == "PNG")
{
#enhancedgreyIMG = ((greyIMG [ , ] + 0.007) * 16) ^ 4
#enhancedgreyIMG = greyIMG [ , ] ^ 0.8
enhancedgreyIMG = ((greyIMG [ , ] - min (greyIMG))*8 )
}
# now find the objects in the image
IMGmask = fillHull (enhancedgreyIMG)
# use a small disk to close gaps in the structures and
# finally create the primary binary matrix from values still >0.3
# this matrix contains all objects, including dizzy background objects
IMGmask = closing (IMGmask, makeBrush (9, shape = 'diamond')) > 0.3
# now find all individual objects being not connected and
# give them an individual ID, thus IMGmask becomes an integer matrix
IMGmask = bwlabel (IMGmask)
# identify contours of all the objects having an ID
IMGcontour = ocontour (IMGmask)
# now get the ID of longest contour
# It is assumed that the largest object in the image is the
# focus object extracted by the LOKI system and we expect
# that this is our object to investigate
IDofLongestContour = which.max (lengths (IMGcontour))
# now we switch back to binary mask
# just containing the largest object
IMGmask = (IMGmask == IDofLongestContour)
# get the dimension of the image for convenient reasons
tmp_IMGwidth = dim (greyIMG) [2]
tmp_IMGheigth = dim (greyIMG) [1]
# create teh first plot with the original image
plot (x = c (1, tmp_IMGwidth),
y = c (1, tmp_IMGheigth),
main = "Original image (distorted aspect ratio)",
xlab = "Horizontal pixel",
ylab = "Vertical pixels",
type = "n")
rasterImage (aSourceImage/max (aSourceImage) , 1, 1, tmp_IMGwidth, tmp_IMGheigth)
plot (x = c (1, tmp_IMGwidth),
y = c (1, tmp_IMGheigth),
main = "Processed image and extracted contour",
xlab = "Horizontal pixel",
ylab = "Vertical pixels",
type = "n")
rasterImage (enhancedgreyIMG/max (enhancedgreyIMG) , 1, 1, tmp_IMGwidth, tmp_IMGheigth)
points ( IMGcontour[[IDofLongestContour]] [ , 2] ,
-IMGcontour[[IDofLongestContour]] [ , 1] + tmp_IMGheigth,
pch = 20,
cex = 0.1,
col = "red")
}
dev.off ()
Projects
Projects (3)
The bachelor's programme of the Jade University of Applied Sciences to achieve the bachelor of engineering degree.
How to become a marine technology engineer (German):
https://www.ingenieur.de/karriere/berufsprofile/beruf-mit-zukunft-so-wird-man-meerestechniker/