Dr. Vibor Laketa

Vibor.Laketa
@med.uni-heidelberg.de
Phone: +49 6221 56–34410

Estab­lish­ment and Appli­ca­tion of
Advanced Microscopy Infrastructure

Projects

Microscopy and infec­tious dis­ease research have been insep­a­ra­ble part­ners ever since in the 1670s Anthonie van Leeuwen­hoek used his new­ly-invent­ed micro­scope to exam­ine a sam­ple of plaque he had scraped from his own teeth, and observed — for the first time — bac­te­ria and oth­er microor­gan­isms that share the world with us. Undoubt­ed­ly, microscopy was fun­da­men­tal in infec­tious dis­ease research, as it was nec­es­sary for the dis­cov­ery of infec­tious agents by direct obser­va­tion and lat­er on also for their diagnosis.

In mod­ern bio­med­ical research that is being real­ized in CIID, microscopy-based exper­i­men­tal approach has a cen­tral role. A com­pre­hen­sive under­stand­ing of host-pathogen inter­ac­tions requires quan­ti­ta­tive assess­ment of mol­e­c­u­lar events across a wide range of spa­tiotem­po­ral scales and orga­ni­za­tion­al com­plex­i­ties Due to recent tech­ni­cal devel­op­ments, this is cur­rent­ly only achiev­able with microscopy. Based on devel­op­ment of new imag­ing modal­i­ties, flu­o­res­cent probes and sen­sors, com­put­er tech­nol­o­gy, image analy­sis algo­rithms and new bio­log­i­cal mod­el sys­tem, the field of bio­log­i­cal microscopy is under­go­ing a rev­o­lu­tion. Only now we are start­ing to appre­ci­ate and make use of the full poten­tial of the microscopy-based exper­i­men­tal approach. Mod­ern micro­scopes have evolved into com­plex robot­ic instru­ments capa­ble of auto­mat­i­cal­ly inter­ro­gat­ing a wide range of bio­log­i­cal process­es at vast­ly dif­fer­ent spa­tiotem­po­ral scales and orga­ni­za­tion­al com­plex­i­ties, from struc­tur­al stud­ies on macro­mol­e­c­u­lar scale all the way to whole organ/body imag­ing in liv­ing animals.

We believe that mod­ern microscopy tech­nol­o­gy is cur­rent­ly unique­ly posi­tioned to pro­pel the infec­tious dis­ease research to a new fron­tier. For these rea­sons, we are estab­lish­ing and apply­ing advanced microscopy infra­struc­ture to allow infec­tious dis­ease research across the range of dif­fer­ent spa­tiotem­po­ral scales and orga­ni­za­tion­al complexities.

More infor­ma­tion about IDIP organ­i­sa­tion and instru­men­ta­tion can be found on the IDIP home­page https://www.idip-heidelberg.org/. If you would like to use the IDIP infra­struc­ture, please fol­low the instruc­tions at https://www.idip-heidelberg.org/usage-concept.

Microscopy Infrastructure under BSL2 and BSL3 Containment

The Infec­tious Dis­ease Imag­ing Plat­form (IDIP) is a sci­en­tif­ic and tech­nol­o­gy plat­form that com­bines advanced microscopy and FACS infra­struc­ture under enhanced biosafe­ty con­di­tions (BSL‑2 and BSL‑3) with project-spe­cif­ic exper­tise and tar­get­ed method­olog­i­cal devel­op­ment for infec­tious dis­ease research, drug dis­cov­ery and diag­nos­tics. More than 250 m² of ground-lev­el (BSL‑2) and under­ground (BSL‑3) space with­in the Cen­ter for Inte­gra­tive Infec­tious Dis­ease Research (CIID) is ded­i­cat­ed to IDIP, encom­pass­ing 14 inter­con­nect­ed microscopy rooms, tis­sue cul­ture and sam­ple prepa­ra­tion facil­i­ties, image analy­sis sta­tions and office areas.

IDIP imple­ments a com­pre­hen­sive range of bioimag­ing tech­nolo­gies span­ning vast­ly dif­fer­ent spa­tial and tem­po­ral scales and lev­els of bio­log­i­cal orga­ni­za­tion, from struc­tur­al stud­ies at the macro­mol­e­c­u­lar scale to whole-organ and in vivo imag­ing. IDIP projects cov­er all aspects nec­es­sary for the exe­cu­tion of microscopy-based exper­i­men­tal approach­es in infec­tious dis­ease research. Activ­i­ties typ­i­cal­ly include:

  • Imple­ment­ing, oper­at­ing and pro­vid­ing advanced microscopy and cell-sort­ing infra­struc­ture under enhanced biosafe­ty con­di­tions (BSL‑2 and BSL‑3).

  • Con­sul­ta­tion dur­ing microscopy-based project plan­ning and exper­i­men­tal design.

  • Col­lab­o­ra­tion in microscopy-based projects con­duct­ed with­in CIID and beyond.

  • Advice and sup­port in image pro­cess­ing, data visu­al­iza­tion and presentation.

  • Devel­op­ment of auto­mat­ed data acqui­si­tion and image-analy­sis workflows.

  • $Coor­di­na­tion of microscopy infra­struc­ture invest­ments and sup­port for relat­ed grant applications.

  • Edu­ca­tion and train­ing in microscopy and relat­ed technologies.

Development of microscopy-based assays for drug screening and diagnostics

Microscopy-based assays pro­vide pow­er­ful approach­es for advanc­ing trans­la­tion­al research, enabling high-con­tent, sin­gle-cell analy­sis of com­plex bio­log­i­cal sys­tems with mul­ti­plexed, scal­able and quan­ti­ta­tive read­outs. This cre­ates new oppor­tu­ni­ties for drug dis­cov­ery and for the devel­op­ment of sen­si­tive, spe­cif­ic and adapt­able diag­nos­tic pro­ce­dures, par­tic­u­lar­ly in the con­text of emerg­ing infec­tious dis­eases and ther­a­peu­tic targets.

By com­bin­ing advanced microscopy with automa­tion, image analy­sis and machine learn­ing, we devel­op microscopy-based assays capa­ble of quan­ti­ta­tive­ly char­ac­ter­iz­ing com­plex cel­lu­lar phe­no­types and respons­es to can­di­date inter­ven­tions. Through ongo­ing col­lab­o­ra­tions, these approach­es are being applied to diverse bio­med­ical chal­lenges in infec­tious dis­eases and beyond, with the aim of devel­op­ing robust, adapt­able and phys­i­o­log­i­cal­ly rel­e­vant assay plat­forms for drug screen­ing and diagnostics.

Heidelberg–Hamburg Infec­tious Dis­eases Imag­ing Asso­ci­a­tion (HHH-IDIA)

HHH-IDIA is a DFG-fund­ed col­lab­o­ra­tive ini­tia­tive con­nect­ing the advanced imag­ing plat­forms in Hei­del­berg and Ham­burg, two sites with a par­tic­u­lar­ly broad and com­ple­men­tary port­fo­lio of imag­ing tech­nolo­gies avail­able under enhanced biosafe­ty con­di­tions. This com­bi­na­tion pro­vides a strong tech­no­log­i­cal basis for advanc­ing microscopy-based infec­tious dis­ease research and address­ing the spe­cif­ic chal­lenges asso­ci­at­ed with imag­ing infec­tious mate­r­i­al under BSL‑3 con­tain­ment. The ini­tia­tive brings togeth­er exper­tise in advanced microscopy, infec­tion biol­o­gy, biosafe­ty and image analysis.

A cen­tral goal of HHH-IDIA is to improve the acces­si­bil­i­ty and appli­ca­tion of advanced BSL‑3 imag­ing tech­nolo­gies with­in the infec­tious dis­ease research com­mu­ni­ty. Through col­lab­o­ra­tion between the par­tic­i­pat­ing sites, HHH-IDIA pro­motes method­olog­i­cal devel­op­ment, knowl­edge exchange and the har­mo­niza­tion of imag­ing approach­es, strength­en­ing the role of advanced microscopy in infec­tious dis­ease research and pan­dem­ic pre­pared­ness. The Hei­del­berg site con­tributes advanced imag­ing exper­tise and infra­struc­ture for the devel­op­ment and appli­ca­tion of microscopy-based approach­es in com­plex mod­el sys­tems. In close col­lab­o­ra­tion with indus­try part­ners, IDIP also eval­u­ates the com­pat­i­bil­i­ty of advanced microscopy sys­tems with decon­t­a­m­i­na­tion pro­ce­dures required for high-con­tain­ment envi­ron­ments, help­ing to facil­i­tate the safe imple­men­ta­tion of emerg­ing imag­ing tech­nolo­gies in BSL‑2 and BSL‑3 research.

Advanced Imag­ing and Cell Sort­ing for Syn­thet­ic Immunol­o­gy (Syn­thIm­mune)

Syn­thIm­mune is a Clus­ter of Excel­lence at Hei­del­berg Uni­ver­si­ty ded­i­cat­ed to devel­op­ing the emerg­ing field of bot­tom-up syn­thet­ic immunol­o­gy. The ini­tia­tive com­bines approach­es from syn­thet­ic biol­o­gy, nan­otech­nol­o­gy, sys­tems biol­o­gy and immunol­o­gy to under­stand, engi­neer and recon­sti­tute immune func­tions, with the long-term goal of devel­op­ing new strate­gies for the pre­ven­tion and treat­ment of infec­tious dis­eases and cancer.

With­in Syn­thIm­mune, IDIP serves as a tech­nol­o­gy plat­form for advanced microscopy and flu­o­res­cence-acti­vat­ed cell sort­ing under enhanced biosafe­ty con­di­tions (BSL‑2 and BSL‑3). The plat­form com­bines spe­cial­ized imag­ing and cell-sort­ing tech­nolo­gies with sup­port through­out the exper­i­men­tal work­flow, from exper­i­men­tal design and method devel­op­ment to data acqui­si­tion, quan­ti­ta­tive image analy­sis and interpretation.

A par­tic­u­lar focus is the devel­op­ment and appli­ca­tion of imag­ing-based approach­es to iden­ti­fy high­ly func­tion­al immune cells and char­ac­ter­ize their behav­iour in phys­i­o­log­i­cal­ly rel­e­vant mod­el sys­tems. Advanced microscopy enables quan­ti­ta­tive analy­sis of immune-cell mor­phol­o­gy, dynam­ics and inter­ac­tions, includ­ing in com­plex three-dimen­sion­al and micro­phys­i­o­log­i­cal mod­els. In com­bi­na­tion with auto­mat­ed image analy­sis and cell sort­ing, these approach­es sup­port the iden­ti­fi­ca­tion and func­tion­al selec­tion of rare immune-cell pop­u­la­tions and pro­vide new oppor­tu­ni­ties for link­ing cel­lu­lar phe­no­types to immune function.

Advanced Imag­ing of Viral Infec­tion and Antivi­ral Drug Dis­cov­ery (SHIELD)

SHIELD – Mol­e­c­u­lar Strate­gies against Viral Entry and Gly­can Shield­ing is a Hori­zon Europe research project inves­ti­gat­ing mech­a­nisms of viral entry, viri­on gly­co­sy­la­tion and immune eva­sion, with the aim of iden­ti­fy­ing and val­i­dat­ing strate­gies to inter­fere with viral infec­tion. By com­bin­ing mol­e­c­u­lar mod­el­ling, struc­tur­al biol­o­gy, virol­o­gy, cel­lu­lar sys­tems and advanced imag­ing, the con­sor­tium inves­ti­gates virus­es with epi­dem­ic and pan­dem­ic poten­tial, includ­ing Las­sa virus (LASV), Hen­dra virus (HeV), Nipah virus (NiV), and the fla­vivirus­es dengue (DENV), West Nile (WNV), Zika (ZIKV) and yel­low fever (YFV).

With­in SHIELD, IDIP devel­ops and applies advanced imag­ing approach­es to inves­ti­gate viral infec­tion dynam­ics across dif­fer­ent stages of the viral life cycle, includ­ing virus–cell inter­ac­tions, entry, intra­cel­lu­lar process­es and the spread of infec­tion in cel­lu­lar and com­plex mod­el sys­tems. A major com­po­nent of the IDIP con­tri­bu­tion is the devel­op­ment of auto­mat­ed and AI-assist­ed work­flows for image acqui­si­tion and analy­sis, enabling unbi­ased quan­ti­ta­tive mea­sure­ments and increased assay through­put. IDIP fur­ther con­tributes to the bench­mark­ing and val­i­da­tion of assay method­olo­gies across the SHIELD con­sor­tium through the exchange of exper­i­men­tal mate­ri­als, inter-lab­o­ra­to­ry com­par­isons and sys­tem­at­ic assess­ment of assay per­for­mance. These activ­i­ties sup­port the estab­lish­ment of robust and trans­fer­able exper­i­men­tal pipelines for the eval­u­a­tion of antivi­ral compounds.

Advanced Imag­ing for Trans­la­tion­al Infec­tious Dis­ease Research (DZIF)

The Ger­man Cen­ter for Infec­tion Research (DZIF) brings togeth­er basic and clin­i­cal research with the goal of trans­lat­ing sci­en­tif­ic dis­cov­er­ies into improved strate­gies for the pre­ven­tion, diag­no­sis and treat­ment of infec­tious dis­eases. A cen­tral chal­lenge in this process is to bridge the gap between mech­a­nis­tic stud­ies in sim­pli­fied exper­i­men­tal sys­tems and the com­plex bio­log­i­cal process­es occur­ring in phys­i­o­log­i­cal­ly rel­e­vant tis­sues and organisms.

With­in DZIF, IDIP sup­ports research in the TTU HIV and oth­er DZIF The­mat­ic Trans­la­tion­al Units, com­bin­ing advanced imag­ing tech­nolo­gies with exper­i­men­tal con­sul­ta­tion, method­olog­i­cal devel­op­ment and quan­ti­ta­tive image analy­sis. The plat­form enables quan­ti­ta­tive inves­ti­ga­tion of pathogen behav­iour and host–pathogen inter­ac­tions in com­plex, close-to-phys­i­o­log­i­cal exper­i­men­tal sys­tems, gen­er­at­ing spa­tial­ly and tem­po­ral­ly resolved data with increased trans­la­tion­al potential.

By enabling infec­tious dis­ease research in increas­ing­ly phys­i­o­log­i­cal­ly rel­e­vant mod­el sys­tems, IDIP con­tributes to bridg­ing the gap between mech­a­nis­tic stud­ies and trans­la­tion­al research. Such approach­es can pro­vide a more direct link between pre­clin­i­cal find­ings and clin­i­cal­ly rel­e­vant biol­o­gy, while also cre­at­ing a tech­no­log­i­cal foun­da­tion for rapid­ly inves­ti­gat­ing emerg­ing pathogens and devel­op­ing new approach­es for infec­tious dis­ease pre­pared­ness and response.