CONTACT
name.su [email protected]
Resea ch G oup Sys ems
Biology / Bioin o ma ics
Re e ences:
[1] Su name, N., Su name, N. N., and Su name, N. N. (2008). Na u e Re iews Immunology
Pic u e o you
CONTACT
Ruman.Ge s @leibniz-hki.de
Resea ch G oup
Applied Sys ems Biology
Re e ences:
[1] Anika Klingbe g e al., “Fully Au oma ed E alua ion o To al Glome ula Numbe and Capilla y Tu
Size in Neph i ic Kidneys Using Ligh shee Mic oscopy,” Jou nal o he Ame ican Socie y o
Neph ology: JASN 28, no. 2 (Feb ua y 2017): 452–59, h ps://doi.o g/10.1681/ASN.2016020232.
[2] Da id Twapoke a Mzinza e al., “Applica ion o Ligh Shee Mic oscopy o Quali a i e and
Quan i a i e Analysis o B onchus-Associa ed Lymphoid Tissue in Mice,” Cellula & Molecula
Immunology, Feb ua y 12, 2018, h ps://doi.o g/10.1038/cmi.2017.150.
Towa ds an open high-pe o mance pla o m o ully-au oma ed
analysis o whole o gan ligh -shee luo escence mic oscopy da a
Ruman Ge s 1,2, Anna Medyukhina1, and Ma c Thilo Figge1,2
1 Applied Sys ems Biology, Leibniz Ins i u e o Na u al P oduc Resea ch and In ec ion Biology – Hans-Knöll-Ins i u e, Jena, Ge many
2 Facul y o Biological Sciences, F ied ich-Schille -Uni e si y Jena, Ge many
5. B onchioles de ec ion module (In p og ess)
Au oma ed assessmen o B onchus-associa ed lymphoid issue (BALT) o
in es iga e lung in ec ion equi es o segmen he b onchioles o he lung,
isible as holes wi h s ong bo de s in LSFM images. We a e cu en ly
de eloping an app oach o segmen hose highly i egula s uc u es.
Ligh -shee luo escence mic oscopy (LSFM) allows quan i a i e h ee-
dimensional analysis o whole o gans. This includes he e alua ion o
s uc u al changes such as a educed numbe o glome uli in kidneys
[1] o he o ma ion o b onchus-associa ed lymphoid issue (BALT)
caused by lung in lamma ion [2].
MISA++
Modula Image S ack Analysis o C++
Implemen ed in mode n C++
Au oma ed pa alleliza ion o wo kloads
Reusable modules o easy ex ension and in eg a ion
Memo y-e icien
Fas
Flexible
MISA++ Lib a y
Tissue de ec ion
Glome uli de ec ion
Tissue de ec ion
MISA++ lib a y
Ex e nal pipeline
Tissue de ec ion
S andalone
Build execu able
Pa ame e documen a ion
MISA++ modules can be used in C++ code o c ea e o he modules o expo ed o a
s andalone execu able ha can be in eg a ed in o o he pipelines o applica ions such as
Fiji/ImageJ.
2. F amewo k o au oma ed analysis
3. Tissue de ec ion module
A B C
2D Segmen ed issue o Lung 🄰 and Kidney 🄱, 🄲
🄰 🄱 🄲
Fu u e: G aph assis ed 3D objec de ec ion
Remo al o alse posi i e 2D issue de ec ion esul s
Quan i ica ion
Numbe o pixels, olume
2D segmen a ion
Algo i hms based on pe cen iles, supe pixels o au o h esholding
In compa ison o he implemen a ion published by Klingbe g e al. [1] (Py hon), MISA++ calcula es he
same wo k up o 148 imes as e i all images a e a ailable a he same ime. I he analysis is done pe
kidney (PK), he calcula ion is s ill app oxima ely 27 imes as e . Pa alleliza ion using 30 h eads.
MISA++
MISA++ (PK)
Py hon
0 1000 2000 3000 4000 5000
26 min
142 min
3907 min
Run ime (min)
Glome uli a e unc ional s uc u es wi hin he enal co ex ha a e
damaged by diseases and oxins [1].
Tissue segmen a ion
MISA++ module
2D glome uli segmen a ion
Klingbe g e al. o Localized O su + Shape
3D objec de ec ion and quan i ica ion
Numbe o glome uli, olume, diame e
Glome uli ( ed) inside he issue (g een)
4. Glome uli de ec ion module
🄳 De ec ion o B onchioles ( ed) inside he issue (g een) su e s om a high numbe o alse
posi i e holes and bo de s, making i di icul o segmen ue posi i e objec s. To sol e his issue,
holes 🄴 a e segmen ed independen ly om bo de s 🄵.
Tissue segmen a ion
MISA++ module
🄳
🄴 🄵
Bo de spli ing
Bo de s (colo ed) sha ed by mul iple holes (black) a e spli be ween he holes.
A g aph is buil , wi h holes and bo de s as edges. The edge weigh is
he numbe o neighbo ing pixels be ween holes/bo de s and o he
backg ound. The sco e o a hole (s a ) is he summa ized low o he
backg ound. The goal is o emo e all B-B edges.
Many common asks o di e en da a
Memo y in ensi e
Long p ocessing
Repea ed code
La ge da ase s
}
1500 350
300 300 2300350
1200 1950
H1 H2
H3B B B B
Backg ound
1200
1950
0
1. Analysis o whole o gans
