Community-developed checklists for publishing images and image analyses.

Schmied C, Nelson MS, Avilov S, Bakker GJ, Bertocchi C, Bischof J, Boehm U, Brocher J, Carvalho MT, Chiritescu C, Christopher J, Cimini BA, Conde-Sousa E, Ebner M, Ecker R, Eliceiri K, Fernandez-Rodriguez J, Gaudreault N, Gelman L, Grunwald D, Gu T, Halidi N, Hammer M, Hartley M, Held M, Jug F, Kapoor V, Koksoy AA, Lacoste J, Le Dévédec S, Le Guyader S, Liu P, Martins GG, Mathur A, Miura K, Montero Llopis P, Nitschke R, North A, Parslow AC, Payne-Dwyer A, Plantard L, Ali R, Schroth-Diez B, Schütz L, Scott RT, Seitz A, Selchow O, Sharma VP, Spitaler M, Srinivasan S, Strambio-De-Castillia C, Taatjes D, Tischer C, Jambor HK

Nature methods, 2023

doi:10.1038/s41592-023-01987-9.

OME-Zarr: a cloud-optimized bioimaging file format with international community support.

Moore J, Basurto-Lozada D, Besson S, Bogovic J, Bragantini J, Brown EM, Burel JM, Casas Moreno X, de Medeiros G, Diel EE, Gault D, Ghosh SS, Gold I, Halchenko YO, Hartley M, Horsfall D, Keller MS, Kittisopikul M, Kovacs G, Küpcü Yoldaş A, Kyoda K, le Tournoulx de la Villegeorges A, Li T, Liberali P, Lindner D, Linkert M, Lüthi J, Maitin-Shepard J, Manz T, Marconato L, McCormick M, Lange M, Mohamed K, Moore W, Norlin N, Ouyang W, Özdemir B, Palla G, Pape C, Pelkmans L, Pietzsch T, Preibisch S, Prete M, Rzepka N, Samee S, Schaub N, Sidky H, Solak AC, Stirling DR, Striebel J, Tischer C, Toloudis D, Virshup I, Walczysko P, Watson AM, Weisbart E, Wong F, Yamauchi KA, Bayraktar O, Cimini BA, Gehlenborg N, Haniffa M, Hotaling N, Onami S, Royer LA, Saalfeld S, Stegle O, Theis FJ, Swedlow JR

Histochemistry and cell biology, 2023

doi:10.1007/s00418-023-02209-1.

CLEMSite, a software for automated phenotypic screens using light microscopy and FIB-SEM.

Serra Lleti JM, Steyer AM, Schieber NL, Neumann B, Tischer C, Hilsenstein V, Holtstrom M, Unrau D, Kirmse R, Lucocq JM, Pepperkok R, Schwab Y

The Journal of cell biology, 2022

doi:10.1083/jcb.202209127.

MoBIE: a Fiji plugin for sharing and exploration of multi-modal cloud-hosted big image data.

Pape C, Meechan K, Moreva E, Schorb M, Chiaruttini N, Zinchenko V, Martinez Vergara H, Mizzon G, Moore J, Arendt D, Kreshuk A, Schwab Y, Tischer C

Nature methods, 2023

doi:10.1038/s41592-023-01776-4.

The Image Data Explorer: interactive exploration of image-derived data.

Muller C, Serrano-Solano B, Sun Y, Tischer C, Hériché JK

PloS one, 2022

doi:10.1371/journal.pone.0273698.

A Hitchhiker's guide through the Bio-image analysis software universe.

Haase R, Fazeli E, Legland D, Doube M, Culley S, Belevich I, Jokitalo E, Schorb M, Klemm A, Tischer C

FEBS letters, 2022

doi:10.1002/1873-3468.14451.

High-speed fluorescence image-enabled cell sorting.

Schraivogel D, Kuhn TM, Rauscher B, Rodríguez-Martínez M, Paulsen M, Owsley K, Middlebrook A, Tischer C, Ramasz B, Ordoñez-Rueda D, Dees M, Cuylen-Haering S, Diebold E, Steinmetz LM

Science (New York, N.Y.), 2022

doi:10.1126/science.abj3013.

Volumetric morphometry reveals spindle width as the best predictor of mammalian spindle scaling.

Kletter T, Reusch S, Cavazza T, Dempewolf N, Tischer C, Reber S

The Journal of cell biology, 2021

doi:10.1083/jcb.202106170.

OME-NGFF: a next-generation file format for expanding bioimaging data-access strategies.

Moore J, Allan C, Besson S, Burel JM, Diel E, Gault D, Kozlowski K, Lindner D, Linkert M, Manz T, Moore W, Pape C, Tischer C, Swedlow JR

Nature methods, 2021

doi:10.1038/s41592-021-01326-w.

Whole-body integration of gene expression and single-cell morphology.

Vergara HM, Pape C, Meechan KI, Zinchenko V, Genoud C, Wanner AA, Mutemi KN, Titze B, Templin RM, Bertucci PY, Simakov O, Dürichen W, Machado P, Savage EL, Schermelleh L, Schwab Y, Friedrich RW, Kreshuk A, Tischer C, Arendt D

Cell, 2021

doi:10.1016/j.cell.2021.07.017.

REMBI: recommended metadata for biological images-enabling reuse of microscopy data in biology.

Sarkans U, Chiu W, Collinson L, Darrow MC, Ellenberg J, Grunwald D, Hériché JK, Iudin A, Martins GG, Meehan T, Narayan K, Patwardhan A, Russell MRG, Saibil HR, Strambio-De-Castillia C, Swedlow JR, Tischer C, Uhlmann V, Verkade P, Barlow M, Bayraktar O, Birney E, Catavitello C, Cawthorne C, Wagner-Conrad S, Duke E, Paul-Gilloteaux P, Gustin E, Harkiolaki M, Kankaanpää P, Lemberger T, McEntyre J, Moore J, Nicholls AW, Onami S, Parkinson H, Parsons M, Romanchikova M, Sofroniew N, Swoger J, Utz N, Voortman LM, Wong F, Zhang P, Kleywegt GJ, Brazma A

Nature methods, 2021

doi:10.1038/s41592-021-01166-8.

An open-source semi-automated robotics pipeline for embryo immunohistochemistry.

Fuqua T, Jordan J, Halavatyi A, Tischer C, Richter K, Crocker J

Scientific reports, 2021

doi:10.1038/s41598-021-89676-5.

Glucocorticoids exacerbate TGFß1 mediated fibrotic signalling in lung fibroblasts by inhibition of metalloproteinase expression and activity.

Khan MM, Zukowska-Kasprzyk J, Neumann B, Halavatyi A, Tischer C, Haberkant P, Stein F, Jung F, Landry J, Lewis J, Pepperkok R

ERJ open research, 2021

doi:10.1183/23120541.lsc-2021.33.

BigDataProcessor2: a free and open-source Fiji plugin for inspection and processing of TB sized image data.

Tischer C, Ravindran A, Reither S, Chiaruttini N, Pepperkok R, Norlin N

Bioinformatics (Oxford, England), 2021

doi:10.1093/bioinformatics/btab106.

Microscopy-based assay for semi-quantitative detection of SARS-CoV-2 specific antibodies in human sera: A semi-quantitative, high throughput, microscopy-based assay expands existing approaches to measure SARS-CoV-2 specific antibody levels in human sera.

Pape C, Remme R, Wolny A, Olberg S, Wolf S, Cerrone L, Cortese M, Klaus S, Lucic B, Ullrich S, Anders-Össwein M, Wolf S, Cerikan B, Neufeldt CJ, Ganter M, Schnitzler P, Merle U, Lusic M, Boulant S, Stanifer M, Bartenschlager R, Hamprecht FA, Kreshuk A, Tischer C, Kräusslich HG, Müller B, Laketa V

BioEssays : news and reviews in molecular, cellular and developmental biology, 2020

doi:10.1002/bies.202000257.

An open-source high-content analysis workflow for CFTR function measurements using the forskolin-induced swelling assay.

Hagemeijer MC, Vonk AM, Awatade NT, Silva IAL, Tischer C, Hilsenstein V, Beekman JM, Amaral MD, Botelho HM

Bioinformatics (Oxford, England), 2020

doi:10.1093/bioinformatics/btaa1073.

An integrated multiomic and quantitative label-free microscopy-based approach to study pro-fibrotic signalling in ex vivo human precision-cut lung slices.

Khan MM, Poeckel D, Halavatyi A, Zukowska-Kasprzyk J, Stein F, Vappiani J, Sevin DC, Tischer C, Zinn N, Eley JD, Gudmann NS, Muley T, Winter H, Fisher AJ, Nanthakumar CB, Bergamini G, Pepperkok R

The European respiratory journal, 2020

doi:10.1183/13993003.00221-2020.

Integrative imaging reveals SARS-CoV-2-induced reshaping of subcellular morphologies.

Cortese M, Lee JY, Cerikan B, Neufeldt CJ, Oorschot VMJ, Köhrer S, Hennies J, Schieber NL, Ronchi P, Mizzon G, Romero-Brey I, Santarella-Mellwig R, Schorb M, Boermel M, Mocaer K, Beckwith MS, Templin RM, Gross V, Pape C, Tischer C, Frankish J, Horvat NK, Laketa V, Stanifer M, Boulant S, Ruggieri A, Chatel-Chaix L, Schwab Y, Bartenschlager R

Cell host & microbe, 2020

doi:10.1016/j.chom.2020.11.003.

Dense and pleiotropic regulatory information in a developmental enhancer.

Fuqua T, Jordan J, van Breugel ME, Halavatyi A, Tischer C, Polidoro P, Abe N, Tsai A, Mann RS, Stern DL, Crocker J

Nature, 2020

doi:10.1038/s41586-020-2816-5.

Tracking cells in epithelial acini by light sheet microscopy reveals proximity effects in breast cancer initiation.

Alladin A, Chaible L, Garcia Del Valle L, Sabine R, Loeschinger M, Wachsmuth M, Hériché JK, Tischer C, Jechlinger M

eLife, 2020

doi:10.7554/eLife.54066.

Genetic screening identifies a SUMO protease dynamically maintaining centromeric chromatin.

Mitra S, Bodor DL, David AF, Abdul-Zani I, Mata JF, Neumann B, Reither S, Tischer C, Jansen LET

Nature communications, 2020

doi:10.1038/s41467-019-14276-x.

Nuclear pores assemble from Nucleoporin condensates during oogenesis.

Hampoelz B, Schwarz A, Ronchi P, Bragulat-Teixidor H, Tischer C, Gaspar I, Ephrussi A, Schwab Y, Beck M

Cell, 2019

doi:10.1016/j.cell.2019.09.022.

The small non-coding vault RNA1-1 acts as a riboregulator of autophagy.

Horos R, Büscher M, Kleinendorst R, Alleaume AM, Tarafder AK, Schwarzl T, Dziuba D, Tischer C, Zielonka EM, Adak A, Castello A, Huber W, Sachse C, Hentze MW

Cell, 2019

doi:10.1016/j.cell.2019.01.030.

Quantification of mouse hematopoietic progenitors' formation using time-lapse microscopy and image analysis.

Bergiers I, Tischer C, Vargel Bölükbaşı Ö, Lancrin C

Bio-protocol, 2019

doi:10.21769/BioProtoc.3137.

Author Correction: A RAB35-p85/PI3K axis controls oscillatory apical protrusions required for efficient chemotactic migration.

Corallino S, Malinverno C, Neumann B, Tischer C, Palamidessi A, Frittoli E, Panagiotakopoulou M, Disanza A, Malet-Engra G, Nastaly P, Galli C, Luise C, Bertalot G, Pece S, Di Fiore PP, Gauthier N, Ferrari A, Maiuri P, Scita G

Nature communications, 2018

doi:10.1038/s41467-018-04515-y.

A RAB35-p85/PI3K axis controls oscillatory apical protrusions required for efficient chemotactic migration.

Salvatore C, Malinverno C, Neumann B, Tischer C, Palamidessi A, Frittoli E, Panagiotakopoulou M, Disanza A, Malet-Engra G, Nastaly P, Galli C, Luise C, Bertalot G, Pece S, Di Fiore PP, Gauthier N, Ferrari A, Maiuri P, Scita G

Nature communications, 2018

doi:10.1038/s41467-018-03571-8.

Dimerization leads to changes in APP (amyloid precursor protein) trafficking mediated by LRP1 and SorLA.

Eggert S, Gonzalez AC, Thomas C, Schilling S, Schwarz SM, Tischer C, Adam V, Strecker P, Schmidt V, Willnow TE, Hermey G, Pietrzik CU, Koo EH, Kins S

Cellular and molecular life sciences : CMLS, 2017

doi:10.1007/s00018-017-2625-7.

Bicarbonate buffered peritoneal dialysis fluid upregulates angiopoietin-1 and promotes vessel maturation.

Eich G, Bartosova M, Tischer C, Wlodkowski TT, Schaefer B, Pichl S, Kraewer N, Ranchin B, Vondrak K, Liebau MC, Hackert T, Schmitt CP

PloS one, 2017

doi:10.1371/journal.pone.0189903.

Acetylated tubulin is essential for touch sensation in mice

Morley SJ, Qi YM, Iovino L, Andolfi L, Guo D, Kalebic N, Castaldi L, Tischer C, Portulano C, Bolasco G, Shirlekar K, Fusco CM, Asaro A, Fermani F, Sundukova M, Matti U, Reymond L, De Ninno A, Businaro L, Johnsson K, Lazzarino M, Ries J, Schwab Y, Hu J, Heppenstall PA

ELIFE, 2016

doi:10.7554/eLife.20813.

A protocol for the systematic and quantitative measurement of protein-lipid interactions using the liposome-microarray-based assay.

Saliba AE, Vonkova I, Deghou S, Ceschia S, Tischer C, Kugler KG, Bork P, Ellenberg J, Gavin AC

Nature protocols, 2016

doi:10.1038/nprot.2016.059.

Reversible chemical dimerizer-induced recovery of PIP2 levels moves clathrin to the plasma membrane.

Schifferer M, Feng S, Stein F, Tischer C, Schultz C

Bioorganic & medicinal chemistry, 2015

doi:10.1016/j.bmc.2015.03.048.

Self-organization of core Golgi material is independent of COPII-mediated endoplasmic reticulum export

Schuberth CE, Tangemo C, Coneva C, Tischer C, Pepperkok R

JOURNAL OF CELL SCIENCE, 2015

doi:10.1242/jcs.154443.

Protein traffic disorders: an effective high-throughput fluorescence microscopy pipeline for drug discovery.

Botelho HM, Uliyakina I, Awatade NT, Proença MC, Tischer C, Sirianant L, Kunzelmann K, Pepperkok R, Amaral MD

Scientific reports, 2015

doi:10.1038/srep09038.

Positive feedback between golgi membranes, microtubules and ER-exit sites directs golgi de novo biogenesis.

Ronchi P, Tischer C, Acehan D, Pepperkok R

Journal of cell science, 2014

doi:10.1242/jcs.150474.

Adaptive fluorescence microscopy by online feedback image analysis.

Tischer C, Hilsenstein V, Hanson K, Pepperkok R

Methods in cell biology, 2014

doi:10.1016/b978-0-12-420138-5.00026-4.

A quantitative liposome microarray to systematically characterize protein-lipid interactions

Saliba AE, Vonkova I, Ceschia S, Findlay GM, Maeda K, Tischer C, Deghou S, van Noort V, Bork P, Pawson T, Ellenberg J, Gavin AC

Nature methods, 2013

doi:10.1038/nmeth.2734.

Molecular recognition of a single sphingolipid species by a protein's transmembrane domain

Contreras FX, Ernst AM, Haberkant P, Björkholm P, Lindahl E, Gönen B, Tischer C, Elofsson A, von Heijne G, Thiele C, Pepperkok R, Wieland F, Brügger B

Nature, 2012

doi:10.1038/nature10742.

Activation of membrane-permeant caged PtdIns(3)P induces endosomal fusion in cells

Subramanian D, Laketa V, Müller R, Tischer C, Zarbakhsh S, Pepperkok R, Schultz C

Nature chemical biology, 2010

doi:10.1038/nchembio.348.

Direct measurement of the nonconservative force field generated by optical tweezers

Wu P, Huang R, Tischer C, Jonas A, Florin EL

Physical review letters, 2009

doi:10.1103/physrevlett.103.108101.

Force- and kinesin-8-dependent effects in the spatial regulation of fission yeast microtubule dynamics

Tischer C, Brunner D, Dogterom M

Molecular systems biology, 2009

doi:10.1038/msb.2009.5.

Chapter 20: Automated spatial mapping of microtubule catastrophe rates in fission yeast

Tischer C, Brunner D, Dogterom M

Methods in cell biology, 2008

doi:10.1016/s0091-679x(08)00620-1.

Quantitative imaging of apoptosis commitment in colorectal tumor cells

Keese M, Offterdinger M, Tischer C, Girod A, Lommerse PH, Yagublu V, Magdeburg R, Bastiaens PI

Differentiation; research in biological diversity, 2007

doi:10.1111/j.1432-0436.2007.00186.x.

Direct observation of nondiffusive motion of a Brownian particle

Lukić B, Jeney S, Tischer C, Kulik AJ, Forró L, Florin EL

Physical review letters, 2005

doi:10.1103/physrevlett.95.160601.

Mechanical properties of single myosin molecules probed with the photonic force microscope

Scholz T, Altmann SM, Antognozzi M, Tischer C, Hörber JK, Brenner B

Biophysical journal, 2005

doi:10.1529/biophysj.104.047795.

Determination and correction of position detection nonlinearity in single particle tracking and three-dimensional scanning probe microscopy

Tischer C, Pralle A, Florin EL

Microscopy and microanalysis : the official journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada, 2004

doi:10.1017/S1431927604040140.

Trapping and tracking a local probe with a photonic force microscope

Rohrbach A, Tischer C, Neumayer D, Florin EL, Stelzer EHK

The Review of scientific instruments, 2004

doi:10.1063/1.1753097.

Lateral phosphorylation propagation: an aspect of feedback signalling?

Tischer C, Bastiaens PI

Nature reviews. Molecular cell biology, 2003

doi:10.1038/nrm1258.

EGFR activation coupled to inhibition of tyrosine phosphatases causes lateral signal propagation

Reynolds AR, Tischer C, Verveer PJ, Rocks O, Bastiaens PI

Nature cell biology, 2003

doi:10.1038/ncb981.

Three-dimensional thermal noise imaging

Tischer C, Altmann S, Fisinger S, Horber JKH, Stelzer EHK, Florin EL

Applied physics letters, 2001

doi:10.1063/1.1423404.