Acquifer IM

Acquifer IM (Imaging Machine) is a fully automated widefield microscope with data storage and processing capabilities ideal for high-content screening assays and phenotypic screening for small-model organisms. Its static sample holder with a mobile optical unit ensures sample stability during imaging, making it ideal for imaging motion-sensitive samples, such as non-adherent cell cultures or embryos.

Intuitive

design

Provides easy, precise, and robust high-content screening and automated microscopy.

Optimal

sample-centered approach

Delivers ideal imaging conditions for sensitive specimens and long-term observations.

Effortless

software workflow

Visualizes large screening datasets and automating centering imaging.

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Features

High-Content Screening

The Acquifer IM is a high-performance solution for screening and high-throughput imaging assays and is compatible with all commonly available multi-well plates (adaptions possible). A host of unique features include built-in temperature regulation, a robotic lid, and an open interface for seamless integration into automated workflows. Its comprehensive data storage and processing integrations are ideal for researchers performing high-content or phenotypic screening.

The software and workflow enable low-magnification pre-screen data of a full microtiter plate to be readily visualized in the Plate-Viewer software on the Acquifer IM high-throughput screening microscope. Different tools and matching algorithms enable the selection of regions of interest (ROIs) for each well and robust autolocalization of target structures for feedback microscopy.

Acquifer IM is optimized for your high-throughput experiments with:

Optimal imaging conditions for sensitive specimens and long-term observations
Uniblock optical design moves to your sample while your sample remains stationary
Built-in temperature control (20 to 40°C) ± 0.5°C homogeneity over whole plate and over time

Automated timelapse microscopy: HeLa cells with H2B-mCherry imaged every 30 minutes for 48 hours. Courtesy of ALMF, EMBL.

Screening workflows for various assay requirements: Cell culture (left) and a zebrafish xenograft assay (right). Courtesy of Arwin Groenewould.

Applications

Zebrafish Imaging

The Acquifer IM is ideally suited for high-throughput screening of zebrafish, an important preclinical model to study development, disease, and molecular and drug screening. The combination of a static sample holder, a mobile optical unit, and built-in temperature regulation ensures specimen stability during imaging.

Embryonic zebrafish xenograft assay of cancer metastasis. Image courtesy of Arwin Groenewoud (Ewa Snaar-Jagalska lab, Leiden University. RGB changed to magenta-green).

High-content screening for chemical modulators of heart development in zebrafish. Images by 4DHeart ESR Eleonora Lupi (Nadia Mercader lab, University of Bern & Acquifer. RGB changed to magenta-green.).

Whole organism screening with organ-specificity in cystic kidney zebrafish disease models. See also: Pandey et al. 2019 (doi: 10.3390/ijms20061290). Image reproduced under CC BY 4.0 DEED.

High content screening in zebrafish for developmental nephrotoxicity of approved drugs. See also: Westhoff et al., 2020. Image reproduced under CC BY.

Organoid Imaging

Acquifer IM provides invaluable insights into cellular structures and dynamic processes, such as tissue morphogenesis, differentiation, and biophysics. With the ability to conduct high-throughput screenings, it supports the study of developing organoids in combination with advanced genome editing techniques and tissue sections.

Fish-derived organoids differentiating into retinal tissue (green). Courtesy of Venera Weinhardt. Zilova et al., 2021. Image reproduced under CC BY 4.0 DEED.

Other Applications

Tissue section of mouse kidney. Courtesy of Maria Bartosova, Uniklinikum Heidelberg, Germany.

Red dogwood (Cornus sanguinea) – 10x objective, 5x5 positions stitched. Courtesy of Mr Göppert, Karlsruhe, Germany.

Specifications

Objective	Magnification	Numerical Aperture	Working Distance
CFI P-Achromat UW2X	2x	0.06	7.5
CFI Plan Fluor4X	4x	0.13	17.2
CFI Plan Fluor10X	10x	0.3	16.0
CFI S P-Fluor ELWD20xC	20x	0.45	8.2-6.9
CFI S P-Fluor ELWD40xC	40x	0.6	3.6-2.8

IM Dimensions: 553mm (21.77") H x 528mm (20.79") W x 555mm (21.85") D

Add-On Module

Photomanipulation

The photomanipulation module was developed in collaboration with Rapp Optoelectronic, Wedel, Germany, who has over 20 years of experience in high-performance photomanipulation and advanced light microscopy techniques.

Its robust design enables researchers to perform advanced experiments with ease. Full datasets of entire microplates can be annotated and subsequently automatically photomanipulated without further user interaction. This enables large scale photomanipulation for various biomedical assays.

The module is an optional hardware upgrade allowing researchers to easily scale-up complex photomanipulation experiments such as photodamaging of cells and tissues, switch convertible fluorophores, uncage compounds or perform optogenetic activation.

Data by Dr. Jana Heigwer (Westhoff Lab, University Children's Hospital, Heidelberg).

Automated Photomanipulation: GFP-positive distal pronephros of a cdh17:egfp transgenic zebrafish with annotated region of interest (left) and after photodamaging (right).

Acquifer IM Control Software

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The Plate-Viewer Software on the Acquifer IM High-Throughput Screening Microscope

Whole Organism Screening: Left: Three day old embryo of the epi:GFP;myl7mR transgenic line. Zebrafish embryos visualized in the Plate-Viewer software after automated ROI selection. Courtesy of Nadia Mercader, Uni Bern. Middle: The red bounding box indicates the field of view of a 10X objective used for subsequent high-resolution imaging. Right: Single z-plane of a high-resolution dataset automatically acquired on the Acquifer IM.

The Plate-Viewer visualization software utilizes data acquired with the Acquifer IM high-throughput screening microscope. The user interface and design allow for intuitive working with datasets, such as overviews of screening data, inspection of individual images and functionalities to adjust channels-display, save data visualizations or time-lapse movies.

Both the system and Plate-Viewer have an open interface that enables automated workflows and feedback-microscopy functionalities.

Conversion and export of images: Export of single z-planes, z-projections, z-stacks or time-series allows for versatility in data analysis. Also, batch export and various file formats (tif, jpeg, png, bmp, mp4) are available.
Feedback Microscopy: Features, such as automated object-detection algorithm and pre-scan ROI-selection enable feedback microscopy.
Plugin Interface: Data processing with external software utilizes a plugin interface. Advanced users can generate their own plugins.

Screenshot of the Plate-Viewer software, showing menus to data as images, stacks, or movies.

Screenshot of the Plate-Viewer software with segmentation based on Stardist/Otsu of nuclei from HeLa cells. Segmentation was performed by calling an external Fiji script via the plugin interface of PV.

Webinars

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On-Demand Session • 55 Minutes

Advances in Microscopy: A Gateway to Enhanced Research, Drug Development, and Diagnostics

Learn about the latest advances in microscopy for enhanced research, drug development, and diagnostics with guest speaker Prof. Nicole Endlich's.

Publications

Year	Journal	Title	Author(s)	Imaging Platform	Subject	Methodology
2025	Zeitschrift für Geburtshilfe und Neonatologie	Automatisierte Laserablation in der Zebrafischlarve als High-Content Modell für die akute Nierenschädigung und epigenetisches Drug-Screening auf regenerationsmodulierende Substanzen	L Rapp, S Sankeert, H Jana, (..) Jens Westhoff	IM	Zebrafischlarve, Epigenetisches Drug-Screening	Automatisierte, Laserablation, High-Content Modell
2024	microPublication Biology	Virtual Orientation Tools (VOTj): Fiji plugins for object centering and alignment	S Sankeert, G Jochen, (..) Laurent Thomas	IM	Standardizing image datasets, Image-processing workflows, Virtual Orientation Tools (VOTj), Fiji plugins	Principal Component Analysis (PCA), Multi-dimensional images
2023	BIOspektrum	In vivo-Medikamenten-Screening zur Behandlung von Glomerulopathien	S Maximilian, B Sophia-Marie, G Jochen, (..) Nicole Endlich	IM	glomerulopathies, Podocyte-related diseases	In vivo drug screening assay, transgenic zebrafish larvae, screening microscopy, Automated quantification
2023	Journal of the American Society of Nephrology	A Novel High-Content Screening Assay Identified Belinostat as Protective in a FSGS—Like Zebrafish Model	S Maximilian, S Florian, L Tim, (..) Nicole Endlich	IM	Embryo implantation, morphogenesis	Mouse, ex vivo, live light-sheet imaging
2023	scientific reports	Identification of side effects of COVID-19 drug candidates on embryogenesis using an integrated zebrafish screening platform	A Ernst, I Piragyte, A Marwa, (..) Nadia Mercader	IM	Embryogenesis, cardiovasculature, COVID-19	Zebrafish embryo model, phenotypic screening
2023	bioRxiv preprint	Natural genetic variation quantitatively regulates heart-rate and -dimension	J Gierten, B Welz, T Fitzgerald, (..) Joachim Wittbrodt	IM	Embryonic heart development,	Japanese rice fish, genetic mapping, inbred vertebrate model
2023	nature methods	EmbryoNet: using deep learning to link embryonic phenotypes to signaling pathways	D Čapek, M Safroshkin, H Morales-Navarrete, (..) Patrick Müller	IM	Signaling pathways, phenotypic defects	Zebrafish, machine learning, automated phenotyping, high-throughput drug screens
2023	Frontiers in Cell and Developmental Biology	pyHeart4Fish: Chamber-specific heart phenotype quantification of zebrafish in high-content screens	V Vedder, T Reinberger, S Haider, (..) Jeanette Erdmann	IM	Cardiac chamber-specific parameters	Automated quantification, drug screen
2022	ScienceDirect	Muscular hydraulics drive larva-polyp morphogenesis	A Stokkermans, A Chakrabarti, K Subramanian, (..) Aissam Ikmi	IM	Morphogenesis, body contractility and motility, muscle hydraulics and organization	cnidarian, quantitative live imaging
2022	Frontiers in Cell and Developmental Biology	The ShGlomAssay Combines High-Throughput Drug Screening With Downstream Analyses and Reveals the Protective Role of Vitamin D3 and Calcipotriol on Podocytes	MC Ristov, T Lange, N Nath, (..) Nicole Endlich	IM	Chronic kidney disease, podocyte de-differentiation	Mouse, high-throughput screening, western blot, RNA sequencing
2022	eLife	Boosting targeted genome editing using the hei-tag	T Thumberger, T Tavhelidse-SuckJose, A Gutierrez-Triana, (..) Joachim Wittbrodt	IM	Genome editing, mRNA	CRISPR, peptide tags,
2021	Journal of the American Society of Nephrology	Glomerular Endothelial Cell-Derived microRNA-192 Regulates Nephronectin Expression in Idiopathic Membranous Glomerulonephritis	J Müller-Deile, N Sopel, A Ohs, (..) Mario Schiffer	IM	idiopathic membranous glomerulonephritis (iMGN), MicroRNA-192-5p	Zebrafish, mice, cell culture, kidney biopsies
2021	International journal of molecular sciences	An Experimental Workflow for Studying Barrier Integrity, Permeability, and Tight Junction Composition and Localization in a Single Endothelial Cell Monolayer: Proof of Concept	M Bartosova, D Ridinger, I Marinovic, (..) Sotirios G. Zarogiannis	IM	Endothelial and epithelial barrier, cell monolayer	Single-molecule localization microscopy, Cell culture, automated imaging and image analysis
2021	eLife	Fish primary embryonic pluripotent cells assemble into retinal tissue mirroring in vivo early eye development	L Zilova, V Weinhardt, T Tavhelidse, (..) Joachim Wittbrodt	IM	Morphogenesis, body contractility and motility, muscle hydraulics and organization	Zebrafish, genome editing, quantitative analysis
2021	PLoS ONE	In vivo identification and validation of novel potential predictors for human cardiovascular diseases	O Hammouda, M Wu, V Kaul, (..) Joachim Wittbrodt	IM	Cardiovascular diseases, genome wide association studies	CRISPR/Cas9 genome editing, automated high-throughput heart rate analysis
2021	F1000Research	Fiji plugins for qualitative image annotations: routine analysis and application to image classification	T Laurent, S Franz, (..) Jochen Gehrig	IM	Fiji, KNIME, image annotation, image classification	Fiji plugins, Principal Component Analysis (PCA)
2020	Cells	A Multiparametric Assay Platform for Simultaneous In Vivo Assessment of Pronephric Morphology, Renal Function and Heart Rate in Larval Zebrafish	P Steenbergen, J Heigwer, G Pandey, (..) Jens Westhoff	IM	Chemical toxicity testing, pronephric phenotypes	Multiparametric in vivo screening pipeline, 3D-printed orientation tool
2020	Frontiers in Cell and Developmental Biology	In vivo High-Content Screening in Zebrafish for Developmental Nephrotoxicity of Approved Drugs	J Westhoff, P Steenbergen, L Thomas, (..) Jochen Gehrig	IM	Nephrotoxic drugs, phenotypic renal alterations	Vertebrate embryos, automated high-content screen, in vivo, microtiter plates
2020	ScienceDirect	The human α-defensin-derived peptide HD5(1–9) inhibits cellular attachment and entry of human cytomegalovirus	R Böffert, R Businger, H Preiß, (..) Michael Schindler	IM	Human cytomegalovirus (HCMV), embryonic development	High-content screening, human cells
2020	scientific reports	Automated high-throughput heartbeat quantification in medaka and zebrafish embryos under physiological conditions	J Gierten, C Pylatiuk, Omar Hammouda, (..) Felix Loosli	IM	Cardiovascular diseases, genome wide association studies	Fish model, screening assay, high-throughput heartbeat analysis
2020	BMC Bioinformatics	Multi-template matching: a versatile tool for object-localization in microscopy images	Laurent Thomas, and Jochen Gehrig	IM	Object-localization	Template matching, multiple template images
2020	microPublication Biology	ImageJ/Fiji ROI 1-click tools for rapid manual image annotations and measurements	Laurent Thomas, and Jochen Gehrig	IM	Manual image annotation, Region of Interest (ROI), ImageJ/Fiji	1-click ROI tools, ImageJ macro language
2019	PLoS ONE	Enhanced in vivo-imaging in medaka by optimized anaesthesia, fluorescent protein selection and removal of pigmentation	C Lischik, L Adelmann, Joachim Wittbrodt	IM	Fluorophore selection, specimen immobilization, elminating pigmentation	in vivo, fish, light-sheet microscopy, gene editing
2019	PLoS ONE	Swift Large-scale Examination of Directed Genome Editing	O Hammouda, F Böttger, J Wittbrodt, Thomas Thumberger	IM	Isolation and detection of alleles, phenotype-genotype correlation	Zebrafish, CRISPR, genetic screening, DIY-pipet tips
2019	International journal of molecular sciences	A Smart Imaging Workflow for Organ-Specific Screening in a Cystic Kidney Zebrafish Disease Model	G Pandey, J Westhoff, F Schaefer, Jochen Gehrig	IM	Glomerular cyst formation, kidney disease	Zebrafish, high-content screening, automated imaging, image analysis
2018	Frontiers in Pediatrics	Zebrafish as a Model for Drug Screening in Genetic Kidney Diseases	G Jochen, P Gunjan, (..) Jens Westhoff	IM	Zebrafish models for inherited kidney disease, Genetic disorders	Automated microscopy, High-throughput and high-content chemical screening
2017	Journal of Cell Biology	Two distinct membrane potential–dependent steps drive mitochondrial matrix protein translocation	A Schendzielorz, C Schulz, O Lytovchenko, (..) Peter Rehling	IM	Organelles, trafficking, translocation	High-content screening
2016	Proceedings of the National Academy of Sciences	δ-COP contains a helix C-terminal to its longin domain key to COPI dynamics and function	E Arakel, K Richter, A Clancy, Blanche Schwappach	IM	Coat protein I (COPI)-coated vesicles, membrane-associated coatomer	High-content screening
2016	scientific reports	Mice lacking WRB reveal differential biogenesis requirements of tail-anchored proteins in vivo	J Rivera-Monroy, L Musiol, K Unthan-Fechner, (..) Fabio Vilardi	IM	Tail-anchored (TA) proteins	Mouse, in-vivo, high-content screening
2014	BMC Biotechnology	Generation of orientation tools for automated zebrafish screening assays using desktop 3D printing	W Jonas, L Urban, (..) Jochen Gehrig	IM	Zebrafish embryo orientation, Morphological phenotypes	Automated screening microscope, 3D-printed orientation tools
2013	PLOS ONE	Development of an Automated Imaging Pipeline for the Analysis of the Zebrafish Larval Kidney	W Jens, G Stefan, S Miriam, (..) Jochen Gehrig	IM	Zebrafish pronephros, Kidney malformation, Nephrotoxic drugs	High-content screening, Automated imaging pipeline, Morpholino-based model

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