CONTACT
[email p o ec ed]
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
[email p o ec ed]
Resea ch G oup
Applied Sys ems Biology
Re e ences:
[1] Rueden, C. T., Schindelin, J., Hine , M. C., DeZonia, B. E., Wal e , A. E., A ena, E. T., & Elicei i, K. W. (2017). ImageJ2: ImageJ o
he nex gene a ion o scien i ic image da a. BMC bioin o ma ics, 18(1), 1-26.
[2] Haase, R., Roye , L. A., S einbach, P., Schmid , D., Dib o , A., Schmid , U., ... & Mye s, E. W. (2020). CLIJ: GPU-accele a ed
image p ocessing o e e yone. Na u e me hods, 17(1), 5-6.
[3] S inge , C., Wang, T., Michaelos, M., & Pachi a iu, M. (2021). Cellpose: a gene alis algo i hm o cellula segmen a ion. Na u e
Me hods, 18(1), 100-106.
JIPipe: Designing au oma ed image analysis
pipelines wi hou p og amming
Ruman Ge s 1,2, Zol án Cse esnyés1, and Ma c Thilo Figge1,3
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
3 Ins i u e o Mic obiology, Facul y o Biological Sciences, F ied ich-Schille -Uni e si y Jena, Ge many
Ja a Image P ocessing Pipeline (JIPipe) is a plugin o ImageJ [1]
ha allows o c ea e image p ocessing pipelines wi hou a sc ip
language. Ins ead use s only ha e o design a low-cha by
connec ing p ocessing s eps (nodes) o each o he in a isual
p og amming language.
🗹 500+ commonly used unc ions om ImageJ and popula plugins
🗹 In ui i e and mode n use in e ace
🗹 Powe ul anno a ion sys em o acking me ada a
🗹 S anda dized & au oma ed ou pu o ha d d i e
JIPipe in eg a es many image analysis unc ions, like image impo ,
h esholding, con as enhancemen , edge de ec ion, o ex ac ing
measu emen s om ImageJ and allows hem o be un in a ba ch
en i onmen . Addi ionally, we included popula plugins like ...
To allow e en g ea e lexibili y, you can u ilize ImageJ Mac o,
Py hon, and R sc ip nodes o w i e o e-use cus om code inside
he JIPipe en i onmen .
Image analysis powe ed by ImageJ
GPU p ocessing and Deep Lea ning
Mo e ea u es ia plugins
JIPipe allows easy u iliza ion o mode n g aphics ha dwa e by
including all unc ions p o ided by he powe ul CLIJ2 [2] lib a y o
GPU p ocessing. JIPipe's ad anced da a managemen
au oma ically akes ca e o all echnical de ails like con e ing
images.
Deep Lea ning has become a commonly used ool in image
analysis. To allow anyone o make use o his echnology, JIPipe
includes Deep Lea ning lib a ies like Cellpose [3] - wi h ull suppo
o all unc ions and pa ame e s, including aining.
A mo e gene alized lib a y o Deep Lea ning using Ke as and
Tenso low is cu en ly being de eloped, as well.
JIPipe al eady p o ides many ea u es, like he able p ocessing
algo i hms, plo ing, so ing and dis ibu ing da a, use in e ac ion
du ing he pipeline, and mo e.
Addi ional ea u es can be easily de eloped in Ja a as ImageJ
plugin, o c ea ed wi hin a GUI ool ha allows anyone o c ea e
new nodes. These a e also au oma ically a ailable om inside
ImageJ, as JIPipe expo s all i s unc ions o ImageJ.
JIPipe comes wi h i s own g aphical use
in e ace ha allows easy access o all unc ions.
① The g aph edi o o build he low cha
② All se ings a e shown on he igh -hand side
① ②
JIPipe al eady in eg a es many popula so wa e
ools like ImageJ and Py hon in o one easy- o-
use en i onmen .
JIPipe comes p e-packaged wi h suppo o GPU
and Deep Lea ning ools like CLIJ and Cellpose.
🗹 Bio-Fo ma s
🗹 OMERO
🗹 Mo phoLibJ
🗹 Fea u eJ
🗹 Mul i-Templa e-Ma ching
Plugins
GUI Edi o
Ja a API
JIPipe can be easily ex ended wi h plugins.
🗹 Nodes
🗹 Da a ypes
🗹 Menus
🗹 ...
