-
Notifications
You must be signed in to change notification settings - Fork 91
/
sites.yml
2108 lines (1900 loc) · 81.9 KB
/
sites.yml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
sites:
- name: "ImageJ"
id: "ImageJ"
url: "https://update.imagej.net/"
description: >-
Base update site for [ImageJ2](https://imagej.net/ImageJ2). No need
to add this to your list of update sites; it is already included.
maintainers:
- "[ImageJ developers](https://imagej.net/Contributors)"
- name: "Fiji"
id: "Fiji"
url: "https://update.fiji.sc/"
description: >-
Base update site for [Fiji](https://imagej.net/Fiji) and
[core Fiji plugins](https://imagej.net/Category:Plugins).
If you [downloaded Fiji directly](https://imagej.net/Downloads),
it is already included.
maintainers:
- "[Fiji developers](https://imagej.net/Contributors)"
- name: "Fiji-Legacy"
id: "Fiji-Legacy"
url: "https://sites.imagej.net/Fiji-Legacy/"
description: >-
Restores old Fiji plugins which never made the transition to Maven, as
well as obsolete libraries no longer used by current Fiji installations.
maintainers:
- "UNSUPPORTED"
- name: "Java-8"
id: "Java-8"
url: "https://sites.imagej.net/Java-8/"
description: >-
Temporary base update site for [ImageJ2](https://imagej.net/ImageJ2) and
[Fiji](https://imagej.net/Fiji) components as everything migrates to Java
8. __Will not work with Java 6 or 7.__
See [this page](https://imagej.net/Java_8) for details.
maintainers:
- "[ImageJ and Fiji developers](https://imagej.net/Contributors)"
- name: "2015-Conference"
id: "2015-Conference"
url: "https://sites.imagej.net/2015-Conference/"
description: >-
A collection of plugins highlighting the latest features of ImageJ. As
seen in [Wayne Rasband](https://imagej.net/Wayne_Rasband)'s
[opening talk](https://vimeo.com/140929691) at the
[2015 conference](https://imagej.net/Conference_2015)!
maintainers:
- "[Curtis Rueden](https://imagej.net/User:Rueden)"
- name: "3D ImageJ Suite"
id: "Tboudier"
url: "https://sites.imagej.net/Tboudier/"
description: >-
A [suite of plugins](https://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:3d_ij_suite:start)
providing enhanced 3D capabilities in ImageJ.
maintainers:
- "[Thomas Boudier](https://imagej.net/User:Tboudier)"
- name: "3Dscript"
id: "3Dscript"
url: "https://romulus.oice.uni-erlangen.de/updatesite/"
description: >-
[3Dscript](https://imagej.net/3Dscript) is a plugin animating 3D/4D microscopy data using a natural-language-based syntax.
maintainers:
- "[Benjamin Schmid](https://imagej.net/User:Bene)"
- name: "ActogramJ"
id: "ActogramJ"
url: "https://romulus.oice.uni-erlangen.de/imagej/updatesites/ActogramJ/"
description: >-
[ActogramJ](https://bene51.github.io/ActogramJ) is a plugin for analyzing actograms.
maintainers:
- "[Benjamin Schmid](https://imagej.net/User:Bene)"
- name: "AIC Janelia - Course"
id: "AICjanelia-course"
url: "https://sites.imagej.net/AICjanelia-course/"
description: >-
A collection of plugins and macros for students of the Advanced Imaging
Center (AIC) Fiji Course.
maintainers:
- "[AIC Janelia](https://imagej.net/User:Aicjanelia)"
- name: "Angiogenesis"
id: "Angiogenesis"
url: "https://sites.imagej.net/Angiogenesis/"
description: >-
A plugin to quantify angiogenic sprout morphology.
maintainers:
- "[Jan Eglinger](https://imagej.net/User:Eglinger)"
- name: "AngioTool"
id: "AngioTool"
url: "https://sites.imagej.net/AngioTool/"
description: >-
The [AngioTool](https://ccrod.cancer.gov/confluence/display/ROB2/Home)
software converted to a Fiji plugin.
maintainers:
- "[Jan Eglinger](https://imagej.net/User:Eglinger)"
- name: "Archipelago"
id: "Lindsey"
url: "https://sites.imagej.net/Lindsey/"
description: >-
A set of plugins that allow Fiji to be run in parallel on a cluster.
Currently,
[Trainable Weka Segmentation](https://imagej.net/Trainable_Weka_Segmentation)
and [Elastic Alignment](https://imagej.net/Elastic_Alignment_and_Montage)
are accelerated in this way.
maintainers:
- "[Larry Lindsey](https://imagej.net/User:Lindsey)"
- name: "AxoNet"
id: "AxoNet"
url: "https://sites.imagej.net/AxoNet/"
description: >-
An implementation of the AxoNet tool which can be used to count axons in
light micrographs of optic nerves.
maintainers:
- "[Matthew Ritch](https://imagej.net/User:Mritch3)"
- name: "BACMMAN"
id: "Ljp"
url: "https://sites.imagej.net/Ljp/"
description: >-
BACteria in Mother Machine ANalyzer: a plugin for high-throughput
analysis of multichannel mother machine data.
See [Sources](https://github.com/jeanollion/bacmman) and [Wiki](https://github.com/jeanollion/bacmman/wiki)
maintainers:
- "Jean Ollion"
- name: "BAR"
id: "Tiago"
url: "https://sites.imagej.net/Tiago/"
description: >-
[BAR](https://imagej.net/BAR) (_Broadly Applicable Routines_) is a
[GitHub-curated](https://github.com/tferr/Scripts) collection of scripts
that simplifies the daily usage of ImageJ. The collection is focused on
Data Analysis, Image Annotation and Segmentation.
maintainers:
- "[Tiago Ferreira](https://imagej.net/User:Tiago)"
- name: "BaSiC"
id: "BaSiC"
url: "https://sites.imagej.net/BaSiC/"
description: >-
[BaSiC](https://www.helmholtz-muenchen.de/icb/research/groups/quantitative-single-cell-dynamics/software/basic/index.html)
is a retrospective image correction method for optical microscopy,
available as a Fiji/ImageJ Plugin. It is based on low rank and sparse
decomposition, which corrects both shading (uneven illumination) in space
and background bleaching in time.
maintainers:
- "[Tingying Peng](mailto:tingying.peng@tum.de)"
- name: "BigDataProcessor"
id: BigDataProcessor"
url: "https://sites.imagej.net/BigDataProcessor/"
description: >-
[BigDataProcessor2](https://github.com/embl-cba/bigDataProcessor2#bigdataprocessor2)
is an Imglib2 and BigDataViewer based tool for inspection and processing of big (TB-sized) image data.
maintainers:
- "[Christian Tischer](mailto:tischitischer@gmail.com)"
- name: "BIG-EPFL"
id: "BIG-EPFL"
url: "https://sites.imagej.net/BIG-EPFL/"
description: >-
ImageJ plugins from
[EPFL's Biomedical Imaging Group (BIG)](https://imagej.net/BIG).
NOT OPEN SOURCE.
maintainers:
- "[Curtis Rueden](https://imagej.net/User:Rueden)"
- name: "BigStitcher"
id: "BigStitcher"
url: "https://sites.imagej.net/BigStitcher/"
description: >-
Based on the HDF5 multi-resolution datastructures of the BigDataViewer
the BigStitcher uses globally optimal registration that is capable of
aligning large multi-tile datasets with high precision and automatic
error detection within just a few minutes while at the same time allowing
for additional user interaction.
maintainers:
- "[Stephan Preibisch](https://imagej.net/User:StephanP)"
- "[David Hörl](https://imagej.net/User:Davidhoerl)"
- name: "BigVolumeViewer Demo"
id: "BigVolumeViewer"
url: "https://sites.imagej.net/BigVolumeViewer/"
description: >-
Demo of BDV volume rendering. See
[this forum post](https://forum.image.sc/t/bigvolumeviewer-tech-demo)
for getting started.
maintainers:
- "[Tobias Pietzsch](https://imagej.net/User:Pietzsch)"
- name: "Bio-Formats"
id: "Bio-Formats"
url: "https://sites.imagej.net/Bio-Formats/"
description: >-
A version of [Bio-Formats](https://imagej.net/Bio-Formats) with the
latest bugfixes from the
[development branch](https://github.com/openmicroscopy/bioformats/tree/develop).
The last SNAPSHOTS are automatically uploaded daily.
maintainers:
- "[OME development team](https://www.openmicroscopy.org)"
- name: "Biomat"
id: "Biomat"
url: "https://sites.imagej.net/Biomat/"
description: >-
Plugins for 3D image preprocessing and detection of fibres in 3D image.
maintainers:
- "[Jiri Janacek](https://imagej.net/User:Biomat)"
- name: "Biomedgroup"
id: "Biomedgroup"
url: "https://sites.imagej.net/Biomedgroup/"
description: >-
A set of plugins developed by the biomedical imaging group of the
dortmund university of applied sciences and arts:
* [Shape Filter](https://imagej.net/Shape_Filter) (Filter binary images by shape),
* [Shape Smoothing](https://imagej.net/Shape_Smoothing) (Smooth objects via Fourier descriptors),
* [Non Local Means Denoise](https://imagej.net/Non_Local_Means_Denoise) (edge preserving noise filter),
* [NanoTrackJ](https://imagej.net/NanoTrackJ) (Size characterization of freely diffusing nanoparticles by particle tracking),
* [Ridge Detection](https://imagej.net/Ridge_Detection) (Line / Ridge detection plugin).
maintainers:
- "[Thorsten Wagner](https://imagej.net/User:Twagner)"
- name: "BioVoxxel"
id: "BioVoxxel"
url: "https://sites.imagej.net/BioVoxxel/"
description: >-
A toolset providing a plugins and macros for flat-field background
corrections, image filters, color coding of shape descriptors and several
tools to process and analyze binary images such as the 'Speckle
Inspector', 'Binary Feature Extractor' and an 'Extended Particle
Analyzer' and a qualitative and quantitative evaluation tool for Fijis'
Auto Threshold methods. More information at the
[BioVoxxel Toolbox](https://imagej.net/BioVoxxel_Toolbox) page and the
[BioVoxxel web site](https://www.biovoxxel.de).
maintainers:
- "[Jan Brocher](https://imagej.net/User:BioVoxxel)"
- name: "Blind Analysis Tools"
id: "Astja"
url: "https://sites.imagej.net/Astja/"
description: >-
Tools to facilitate blind i.e., unbiased analysis of (image) data.
For more information visit the
[documentation page](https://imagej.net/Blind_Analysis_Tools).
maintainers:
- "[Astha Jaiswal](https://imagej.net/User:Astja), Holger Lorenz"
- name: "BoneJ"
id: "BoneJ"
url: "https://sites.imagej.net/BoneJ/"
description: >-
A collection tools for trabecular geometry and whole bone shape analysis.
This update site hosts the new experimental, modernized version of BoneJ
that works with the latest Fiji. Enabling the update site creates the
menu entries Plugins > BoneJ. The pQCT tools are now hosted on their own
update site (see below).
maintainers:
- "[Michael Doube](https://imagej.net/User:Michaeldoube)"
- "[Alessandro Felder](https://imagej.net/User:Alessandrofelder)"
- name: "CALM"
id: "CALM"
url: "https://sites.imagej.net/CALM/"
description: >-
Plugins from the Crick Advanced Light Microscopy Facility at
[The Francis Crick Institute](https://www.crick.ac.uk).
maintainers:
- "[David Barry](mailto:david.barry@crick.ac.uk)"
- name: "CAMDU"
id: "CAMDU"
url: "https://sites.imagej.net/CAMDU/"
description: >-
Plugins from the
[Computing and Advanced Microscopy Development Unit](https://www.warwick.ac.uk/camdu)
at the [University of Warwick](https://www.warwick.ac.uk).
maintainers:
- "[Erick Martins Ratamero](mailto:e.martins-ratamero.1@warwick.ac.uk)"
- name: "CATS"
id: "CATS"
url: "https://sites.imagej.net/CATS/"
description: >-
Context Aware Trainable Segmentation [CATS](https://github.com/embl-cba/cats)
maintainers:
- "[Christian Tischer](mailto:tischitischer@gmail.com)"
- name: "CellTrackingChallenge"
id: "Ulman"
url: "https://sites.imagej.net/Ulman/"
description: >-
Implementation of measures and front-end plugins used in and related to
the [Cell Tracking Challenge](http://www.celltrackingchallenge.net).
maintainers:
- "[Vladimír Ulman](mailto:ulman@mpi-cbg.de)"
- name: "CIP"
id: "CIP"
url: "https://sites.imagej.net/CIP/"
description: >-
[An image procesing toolbox focused on scripting](https://imagej.net/CIP).
maintainers:
- "[Benoit Lombardot](https://imagej.net/User:Benoit)"
- name: "CircleSkinner"
id: "CircleSkinner"
url: "https://sites.imagej.net/CircleSkinner/"
description: >-
A Fiji plugin for the automated detection and quantification of circular
structures in images.
maintainers:
- "[Jean-Yves Tinevez](https://imagej.net/User:JeanYvesTinevez)"
- name: "clij"
id: "clij"
url: "https://sites.imagej.net/clij/"
description: >-
GPU-acceleration for ImageJ.
See [https://clij.github.io/](https://clij.github.io/)
maintainers:
- "[Robert Haase](https://imagej.net/User:Haesleinhuepf)"
- name: "clij2"
id: "clij2"
url: "https://sites.imagej.net/clij2/"
description: >-
Experimental update site / incubator for the future release of clij2.
See [https://clij.github.io/clij-advanced-filters](https://clij.github.io/clij-advanced-filters)
maintainers:
- "[Robert Haase](https://imagej.net/User:Haesleinhuepf)"
- name: "ClearVolume"
id: "ClearVolume"
url: "https://sites.imagej.net/ClearVolume/"
description: >-
ClearVolume is a fast 3D viewer, for more information see also the
[ClearVolume wiki](https://github.com/ClearVolume/ClearVolume/wiki).
maintainers:
- "[ClearVolume](https://imagej.net/User:ClearVolume)"
- name: "CMCI-EMBL"
id: "Miura"
url: "https://sites.imagej.net/Miura/"
description: >-
A plugin for loading sample images and misc functionality for CMCI ImageJ
course. See [CMCI course](http://wiki.cmci.info/mainpages/courses).
Eventually more plugins will be added.
maintainers:
- "[Kota Miura](https://imagej.net/User:Miura)"
- name: "CMP-BIA tools"
id: "CMP-BIA"
url: "https://sites.imagej.net/CMP-BIA/"
description: >-
The development version of
[CMP-BIA tools](https://imagej.net/CMP-BIA_tools).
maintainers:
- "[Jiri Borovec](http://cmp.felk.cvut.cz/~borovji3/)"
- name: "CMTK Registration"
id: "Jefferis"
url: "https://sites.imagej.net/Jefferis/"
description: >-
CMTK Registration GUI.
maintainers:
- "[Gregory Jefferis](https://imagej.net/User:Jefferis)"
- name: "Colocalization by Cross Correlation"
id: "Amccall"
url: "https://sites.imagej.net/Amccall/"
description: >-
A co-localization plugin that attempts to find non-random spatial correlations
between two images and provide an estimate of their distance and standard deviation.
Conceptually similar to Van Steensel's CCF. For more details see our
[wiki page](https://imagej.net/Colocalization_by_Cross_Correlation).
maintainers:
- "[Andrew McCall](https://imagej.net/User:Amccall)"
- name: "Cookbook"
id: "Cookbook"
url: "https://sites.imagej.net/Cookbook/"
description: >-
Plugins from the [Cookbook](https://imagej.net/Cookbook).
maintainers:
- "[Cookbook Team](https://imagej.net/Cookbook#Credits)"
- name: "CSBDeep"
id: "CSBDeep"
url: "https://sites.imagej.net/CSBDeep/"
description: >-
Plugins for executing pretrained CARE networks.
maintainers:
- "[Deborah Schmidt](https://imagej.net/User:Frauzufall)"
- name: "CSIM Laboratory"
id: "Acsenrafilho"
url: "https://sites.imagej.net/Acsenrafilho/"
description: >-
A set of plugins, macros and scripts developed by the CSIM (Computing in
Signal and Images in Medicine) research group. One of the methods
available are
[Anomalous Diffusion Filters](https://imagej.net/Anomalous_Diffusion_Filters),
[Noise Generator](https://imagej.net/Noise_Generator),
[MRI Perfusion](https://imagej.net/MRI_Perfusion) and the
[Sample Entropy for Images](https://imagej.net/SampEn2D).
Please, see the [CSIM group web page](https://imagej.net/CSIMLab)
to find out how the methods works and more information about us.
maintainers:
- "[Antonio Carlos da S. Senra Filho](https://imagej.net/User:Acsenrafilho)"
- name: "CWNS dense nuclei segmenter"
id: "CWNS"
url: "https://sites.imagej.net/CWNS/"
description: >-
The Fiji implementation of the CWNS dense nuclei segmenter, presented in
["Object Segmentation and Ground Truth in 3D Embryonic Imaging"](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0150853),
by B. Rajasekaran et al., Plos ONE, 2016.
maintainers:
- "[Jean-Yves Tinevez](https://imagej.net/User:JeanYvesTinevez)"
- name: "DeepClas4Bio-plugins"
id: "Adines"
url: "https://sites.imagej.net/Adines/"
description: >-
Collection of plugins that use
[DeepClas4Bio API](https://github.com/adines/DeepClas4Bio) --
an API that facilitates the interoperability of bioimaging tools with
deep learning frameworks.
maintainers:
- "[Adrián Inés](mailto:adines@unirioja.es)"
- name: "DHM Utilities"
id: "Sudgy"
url: "https://sites.imagej.net/Sudgy/"
description: >-
Collection of plugins for use in digital holographic microscopy, such as
hologram reconstruction, numerical propagation, and phase unwrapping.
maintainers:
- "[David Cohoe](mailto:dcohoe@pdx.edu)"
- name: "DiameterJ"
id: "DiameterJ"
url: "https://sites.imagej.net/DiameterJ/"
description: >-
Macros for quantitative analysis of nanofiber images. DiameterJ is able
to analyze any network of connecting lines (validated for SEM micrographs
of micro- and nanofibers) and produce metrics such as mean diameter,
histograms of fiber diameter, mean pore size, histogram of all pore
areas, percent porosity, etc. See [soon](coming) for more information
and the publication describing how DiameterJ works and its limitations.
maintainers:
- "[Nathan Hotaling](https://imagej.net/User:DiameterJ)"
- name: "DiversePathsJ"
id: "Vuhlmann"
url: "https://sites.imagej.net/Vuhlmann/"
description: >-
DiversePathsJ implements a dynamic programming approach for the general
task of finding diverse shortest paths between two end-points. It is not
linked to a specific biological problem and can be applied to a large
variety of images. See the [DiversePathsJ web
page](http://bigwww.epfl.ch/algorithms/diversepathsj/) for more
information.
maintainers:
- "[Virginie Uhlmann](https://imagej.net/User:Vuhlmann)"
- name: "EMBL-CBA"
id: "EMBL-CBA"
url: "https://sites.imagej.net/EMBL-CBA/"
description: >-
Collection of image visualisation, processing, registration and analysis tools.
maintainers:
- "[Christian Tischer](mailto:tischitischer@gmail.com)"
- "[EMBL-CBA](mailto:image-analysis-support@embl.de)"
- name: "EpiGraph"
id: "Pedgomgal1"
url: "https://sites.imagej.net/Pedgomgal1/"
description: >-
EpiGraph: an open-source method to quantify epithelial organization.
EpiGraph is a Fiji plugin that combines computational geometry and graph
theory to measure organization in any computational or natural
tessellation image.
maintainers:
- "[Pedro J. Gómez Gálvez](mailto:pgomez-ibis@us.es)"
- "[Pablo Vicente Munuera](https://github.com/Pablo1990)"
- name: "ElastixWrapper"
id: "ElastixWrapper"
url: "https://sites.imagej.net/ElastixWrapper/"
description: >-
Image registration using [elastix](http://elastix.isi.uu.nl/)
maintainers:
- "[Christian Tischer](mailto:tischitischer@gmail.com)"
- name: "EM Tool"
id: "IMBalENce"
url: "https://sites.imagej.net/IMBalENce/"
description: >-
[EM tool](https://imagej.net/IMBalENce) is a suite of simple tools for electron microscopist
maintainers:
- "[Zhou Xu](mailto:zhou.xu@monash.edu)"
- name: "EZFig"
id: "EZF"
url: "https://sites.imagej.net/EZF/"
description: >-
EZFig is a tool to build publication-ready scientific figures based on
ScientiFig but simpler to use. It must be used in combination with the
'Java-8' update site.
maintainers:
- "[Benoit Aigouy](mailto:scientifig@gmail.com)"
- name: "FAST"
id: "FAST"
url: "https://sites.imagej.net/FAST/"
description: >-
Fluorescence image AnalysiS Tool automates tasks to process a set of
single-channel fluorescence images.
maintainers:
- "[C.TURIÈS](https://imagej.net/User:C.TURIÈS)"
- name: "FFMPEG"
id: "FFMPEG"
url: "https://fiji.sc/~schindelin/ffmpeg-plugins/"
description: >-
Fiji plugins which allow reading and writing to
[FFmpeg](https://www.ffmpeg.org/)-supported formats via native bindings.
maintainers:
- "[Curtis Rueden](https://imagej.net/User:Rueden)"
- name: "FibrilJ"
id: "FibrilJ"
url: "https://sites.imagej.net/FibrilJ/"
description: >-
Macros developed to measure the diameters and persistence lengths if
amyloids fibrils by AFM, EM, STM etc. iamges. It provides histogram
distribution of the average fibril diameter and average fibril
persistence length. Was validated for AFM, SEM and TEM images of Sup35NM
fibrils on mica, silicon, gold surfaces and formvar film.
maintainers:
- "Petr Sokolov"
- name: "FilamentDetector"
id: "FilamentDetector"
url: "https://sites.imagej.net/FilamentDetector/"
description: >-
A Fiji plugin that allows easy, fast and accurate detection and tracking
of biological filaments.
maintainers:
- "[Hadrien Mary](https://imagej.net/User:Hadim)"
- name: "Filopodyan"
id: "Rb7777"
url: "https://sites.imagej.net/Rb7777/"
description: >-
Filopodia dynamics analysis. See
[GitHub](https://github.com/gurdon-institute/Filopodyan) for the user
guide, source code and R scripts for downstream analysis.
maintainers:
- "Richard Butler"
- "Vasja Urbančič"
- name: "FiloQuant"
id: "FiloQuant"
url: "https://sites.imagej.net/FiloQuant/"
description: >-
[FiloQuant](https://imagej.net/User:FiloQuant) is a user friendly and
modifiable tool for automated detection and quantification of filopodia
properties such as length and density. FiloQuant can also track
filopodia.
maintainers:
- "Guillaume Jacquemet"
- "Alexandre Carisey"
- name: "FPBioimage"
id: "Fpbioimage"
url: "https://sites.imagej.net/Fpbioimage/"
description: >-
A plugin to prepare and upload data for
[Fpbioimage](https://imagej.net/Fpbioimage).
maintainers:
- "[FPBioimage](https://imagej.net/User:Fpbioimage)"
- name: "FracLac Suite"
id: "Akarperien"
url: "https://sites.imagej.net/Akarperien/"
description: >-
Fractal Analysis and Modelling tools for neuroscience and other
disciplines. __Analysis:__ <abbr title=\"Box Counting Fractal
Dimension\">D<sub>B</sub></abbr>, <abbr title=\"Fixed Grid and Sliding
Box\">lacunarity</abbr>, multifractal spectra, <abbr title=\"Local
Connected Fractal Dimension\">D<sub>LC</sub></abbr>, <abbr title=\"Mass
vs Distance Dimension\">D<sub>MvD</sub></abbr>, subscanning, and
graphical wave analysis for binary and gray scale images, with inline and
[online](https://imagej.net/plugins/fraclac/FLHelp/Introduction.htm)
theoretical and practical help. __Outputs:__ detailed analyses, raw
data, plots, colour-coding, and settings (*.fl) files. __Modelling:__
benchmark fractals, natural structures (e.g., neurons), megadata to
graphical wave images. Code in jar. See
[citations](https://imagej.net/plugins/fraclac/FLHelp/FLCitations.htm).
maintainers:
- "[A. Karperien](https://imagej.net/User:Akarperien)"
- name: "FunImageJ"
id: "FunImageJ"
url: "https://sites.imagej.net/FunImageJ/"
description: >-
Fiji plugin that provides Clojure wrappings of many commonly used
functions from ImageJ and ImgLib2. Works with SciJava scripting for
Clojure. FunImageJ scripts can be converted into standalone
ImageJ/Fiji-based programs. Code available
[on GitHub](https://github.com/kephale/fun.imagej).
maintainers:
- "[Kyle Harrington](https://imagej.net/User:Kharrington)"
- name: "Fuzzy logic and artificial neural networks image processing toolbox for ImageJ"
id: "Astartes91"
url: "https://sites.imagej.net/Astartes91/"
description: >-
Toolbox includes fuzzy edge detection plugin, fuzzy contrast enhancement
plugin and ann edge detection plugin. Source code
[on GitHub](https://github.com/astartes91/imagej-neural-fuzzy-plugins).
maintainers:
- "[Vladimir Nizamutdinov](mailto:astartes91@gmail.com)"
- name: "Fuzzy Set"
id: "Rerger"
url: "https://sites.imagej.net/Rerger/"
description: >-
[Fuzzy Set](https://imagej.net/User:Rerger) is an ImageJ plugin, to
transform the intensity of the image using Fuzzy Sets.
maintainers:
- "[Robert Erger](mailto:rerger@leomail.tamuc.edu)"
- name: "GDSC"
id: "GDSC"
url: "https://sites.imagej.net/GDSC/"
description: >-
The Genome Damage and Stability Centre (GDSC) plugins are a collection of
analysis programs for microscopy images including colocalisation analysis
and peak finding (FindFoci). See
[GDSC Plugins](http://www.sussex.ac.uk/gdsc/intranet/microscopy/UserSupport/AnalysisProtocol/imagej/gdsc_plugins/)
for details.
maintainers:
- "[Alex Herbert](mailto:a.herbert@sussex.ac.uk)"
- name: "GDSC-SMLM"
id: "GDSC-SMLM"
url: "https://sites.imagej.net/GDSC-SMLM/"
description: >-
Tools for Single Molecule Light Microscopy (SMLM). This version has been
superceded by GDSC-SMLM2; the two versions cannot be used together.
The original [user manual](http://www.sussex.ac.uk/gdsc/intranet/pdfs/SMLM.pdf)
is available.
maintainers:
- "[Alex Herbert](mailto:a.herbert@sussex.ac.uk)"
- name: "GDSC-SMLM2"
id: "GDSC-SMLM2"
url: "https://sites.imagej.net/GDSC-SMLM2/"
description: >-
Tools for Single Molecule Light Microscopy (SMLM) including PALM,
STORM and other single molecule microscopy methods.
See the latest documentation on [ReadTheDocs](https://gdsc-smlm.readthedocs.io/).
maintainers:
- "[Alex Herbert](mailto:a.herbert@sussex.ac.uk)"
- name: "Hadim"
id: "Hadim"
url: "https://sites.imagej.net/Hadim/"
description: >-
Contains the ij2-python-lib package.
maintainers:
- "[Hadrien Mary](https://imagej.net/User:Hadim)"
- name: "HDF5"
id: "Ronneber"
url: "https://sites.imagej.net/Ronneber/"
description: >-
The HDF5 plugin allows to load and save data in HDF5 format.
For details see
[HDF5 plugin](https://lmb.informatik.uni-freiburg.de/resources/opensource/imagej_plugins/hdf5.html).
maintainers:
- "[Olaf Ronneberger](mailto:ronneber@informatik.uni-freiburg.de)"
- name: "HistoJ"
id: "Pathomation"
url: "https://sites.imagej.net/Pathomation/"
description: >-
Plugin to interface with
[Pathomation's digital slide viewer](https://www.pathomation.com/)
which can open Olympus VSI (.vsi), Ventana / Roche BIF (.bif),
Hamamatsu NDPI (.ndpi), 3DHistech MRXS (.mrxs),
Aperio / Leica SVS (.svs), Leica SCN (.scn), Carl Zeiss ZVI (.zvi),
Carl Zeiss CZI (.czi), Nikon ND2 (.nd2), Sakura SVSlide (.svslide).
maintainers:
- "[Pathomation](mailto:info@pathomation.com)"
- name: "Hohlbein Lab"
id: "HohlbeinLab"
url: "https://sites.imagej.net/HohlbeinLab/"
description: >-
Plugins created by the [Hohlbein Lab](https://jhohlbein.com/) (Wageningen University,
Laboratory of Biophysics). Includes ThunderSTORM with added [phasor-based
localization](https://aip.scitation.org/doi/abs/10.1063/1.5005899) for
single-molecule microscopy analysis (pSMLM-3D, Martens et al., JCP, 2018).
maintainers:
- "[Koen Martens](mailto:koen.martens@wur.nl)"
- "[Johannes Hohlbein](mailto:johannes.hohlbein@wur.nl)"
- name: "IamMM"
id: "IamMM"
url: "https://sites.imagej.net/IamMM/"
description: >-
[Image Synthesizer](https://imagej.net/Image_Synthesizer) (plugin to
generate images from mathematical functions and conditional statements in
a coordinate system independent from the aspect ratio or image size),
[Spheroid RGB](https://github.com/IamMM/Spheroid_RGB) (plugin to analyze
microscopy RGB images with fluorescent stained cells)
maintainers:
- "[Maximilian Maske](mailto:m.maske@posteo.de Maximilian Maske)"
- name: "IBMP-CNRS"
id: "Mutterer"
url: "https://sites.imagej.net/Mutterer/"
description: >-
[FigureJ](https://imagejdocu.tudor.lu/doku.php?id=plugin:utilities:figurej:start)
(easy article figure creation),
[ActionBar](https://imagejdocu.tudor.lu/doku.php?id=plugin:utilities:action_bar:start)
(macro-based buttons bars),
[Droplet](https://imagejdocu.tudor.lu/doku.php?id=plugin:utilities:droplet:start)
(drag and drop file processor), LSM Reader and LSM Toolbox moved to the
main Fiji update site,
[IJ_Ed](https://imagejdocu.tudor.lu/doku.php?id=plugin:utilities:ij_ed:start)
(jEdit link).
maintainers:
- "[Jerome Mutterer](mailto:jerome.mutterer@gmail.com)"
- name: "IJ-OpenCV-plugins"
id: "IJ-OpenCV"
url: "https://sites.imagej.net/IJ-OpenCV/"
description: >-
Collection of plugins created using the
[IJ-OpenCV library](https://github.com/joheras/IJ-OpenCV) --
a library that allows the connection of ImageJ and OpenCV.
maintainers:
- "[Jónathan Heras](mailto:joheras@gmail.com)"
- name: "IJMMD"
id: "IJMMD"
url: "https://sites.imagej.net/IJMMD/"
description: >-
[ImageJ Macro Markdown](https://github.com/haesleinhuepf/imagejmacromarkdown)
scripting language interpreter to create
notebook-like pages using ImageJ Macro and Markdown.
maintainers:
- "[Robert Haase](https://imagej.net/User:Haesleinhuepf)"
- name: "IJPB-plugins"
id: "IJPB-plugins"
url: "https://sites.imagej.net/IJPB-plugins/"
description: >-
Collection of plugins created at the INRA-IJPB Modeling and Digital
Imaging lab to perform 2D/3D image segmentation, fast morphological
operations and geometric analysis
maintainers:
- "[Modeling and Digital Imaging lab, INRA-Versailles](https://www-ijpb.versailles.inra.fr/en/bc/equipes/modelisation-imagerie/)"
- name: "ilastik"
id: "Ilastik"
url: "https://sites.imagej.net/Ilastik/"
description: >-
Provides interoperability between Fiji and ilastik workflows
(pixel/object classification, tracking) as well as HDF5 file
export/import.
maintainers:
- "[Adrian Wolny](mailto:adrian.wolny@iwr.uni-heidelberg.de)"
- name: "ImageJ Latex"
id: "Yul.liuyu"
url: "https://sites.imagej.net/Yul.liuyu/"
description: >-
Add math equations to an image using Latex.
maintainers:
- "[Yu Liu](https://imagej.net/User:Yul.liuyu)"
- name: "ImageJ-ITK"
id: "ImageJ-ITK"
url: "https://sites.imagej.net/ImageJ-ITK/"
description: >-
Adds [ITK integration](https://github.com/imagej/imagej-itk) including
conversion between [ITK](http://www.simpleitk.org/) and
[ImageJ](https://github.com/imagej/imagej) images. See the
[ITK page](https://imagej.net/ITK) for more information.
maintainers:
- "[Curtis Rueden](https://imagej.net/User:Rueden)"
- name: "ImageJ-MATLAB"
id: "MATLAB"
url: "https://sites.imagej.net/MATLAB/"
description: >-
Adds support for MATLAB
[scripting](https://github.com/scijava/scripting-matlab) and converting
between MATLAB arrays and
[ImageJ](https://github.com/imagej/imagej-matlab) components. See the
[scripting tutorial](https://imagej.net/MATLAB) for more information.
maintainers:
- "[Mark Hiner](https://imagej.net/User:Hinerm)"
- name: "ImageScience"
id: "ImageScience"
url: "https://sites.imagej.net/ImageScience/"
description: >-
Base update site for all [ImageScience](https://imagej.net/ImageScience)
related ImageJ plugins.
maintainers:
- "[Erik Meijering](https://imagej.net/User:ImageScience)"
- name: "ImagingBook"
id: "ImagingBook"
url: "https://sites.imagej.net/ImagingBook/"
description: >-
Common ImageJ/Java source code for the
[Digital Imaging books](https://imagingbook.com) by
[Wilhelm Burger](https://imagej.net/User:ImagingBook) and Mark J. Burge.
This update site only provides the common "imagingbook" LIBRARY plus
required third-parts JAR files. Specific sets of demo plugins are
available for each book edition; choose ONE of the update sites listed
below. Find the online documentation and additional materials
[on the SourceForge page](https://sourceforge.net/projects/imagingbook/).
maintainers:
- "[Wilhelm Burger](https://imagej.net/User:ImagingBook)"
- name: "ImagingBookEn1"
id: "ImagingBookEn1"
url: "https://sites.imagej.net/ImagingBookEn1/"
description: >-
ImageJ PLUGINS (only) for "Digital Image Processing – An Algorithmic
Introduction Using Java" by W. Burger & M. Burge, Springer (2008).
maintainers:
- "[Wilhelm Burger](https://imagej.net/User:ImagingBook)"
- name: "ImagingBookEn2"
id: "ImagingBookEn2"
url: "https://sites.imagej.net/ImagingBookEn2/"
description: >-
ImageJ PLUGINS (only) for "Principles of Digital Image Processing" (Vols.
1–3) by W. Burger & M. Burge, Springer (2009–2013).
maintainers:
- "[Wilhelm Burger](https://imagej.net/User:ImagingBook)"
- name: "ImagingBookEn3"
id: "ImagingBookEn3"
url: "https://sites.imagej.net/ImagingBookEn3/"
description: >-
ImageJ PLUGINS (only) for "Digital Image Processing – An Algorithmic
Introduction Using Java" by W. Burger & M. Burge, 2nd ed., Springer
(2016).
maintainers:
- "[Wilhelm Burger](https://imagej.net/User:ImagingBook)"
- name: "ImagingBookDe2"
id: "ImagingBookDe2"
url: "https://sites.imagej.net/ImagingBookDe2/"
description: >-
ImageJ PLUGINS (only) for "Digitale Bildverarbeitung – Eine Einführung
mit Java und ImageJ" by W. Burger & M. Burge, Springer (2006).
maintainers:
- "[Wilhelm Burger](https://imagej.net/User:ImagingBook)"
- name: "ImagingBookDe3"
id: "ImagingBookDe3"
url: "https://sites.imagej.net/ImagingBookDe3/"
description: >-
ImageJ PLUGINS (only) for "Digitale Bildverarbeitung – Eine
algorithmische Einführung mit Java" by W. Burger & M. Burge, Springer
(2015).
maintainers:
- "[Wilhelm Burger](https://imagej.net/User:ImagingBook)"
- name: "ImagingFCS"
id: "ImagingFCS"
url: "https://sites.imagej.net/ImagingFCS/"
description: >-
Imaging_FCS 1.491 is a basic ImageJ plugin to calculate and view
spatio-temporal correlation functions from 16 bit gray tiff stack files.
It was written under FIJI (ImageJ 1.51f; Java 1.8.0_102) and requires
Imagescience for statistics (simulator) and Apache Poi for file reading
and writing.
maintainers:
- "[Thorsten Wohland](http://www.dbs.nus.edu.sg/lab/BFL/imfcs_image_j_plugin.html)"
- name: "IMCF Uni Basel"
id: "UniBas-IMCF"
url: "https://sites.imagej.net/UniBas-IMCF/"
description: >-
Various plugins (most notably the Stitching-Wrapper for Olympus FluoView
OIF / OIB mosaics), macros and Action Bars, including a LUT selection bar
that lets you click on a visual representation of the LUT. Also ships the
[MultiStackRegistration](https://github.com/miura/MultiStackRegistration)
plugin (the version modified by Kota Miura that is usable from scripts).
maintainers:
- "[Niko Ehrenfeuchter](https://imagej.net/User:Ehrenfeu)"
- name: "IMOD-ZOLA"
id: "IMOD-ZOLA"
url: "https://sites.imagej.net/IMOD-ZOLA/"
description: >-
Zernike Optimized Localization Algorithm for 3D single molecule
localizations [ZOLA-3D](https://github.com/imodpasteur/ZOLA-3D)
developed in Institut Pasteur, group IMOD -- a CUDA-enabled localization
algorithm for extended PSF single-molecule localization microscopy. Paper
is under review.
maintainers:
- "[Andrey Aristov](mailto:aaristov@pasteur.fr)"
- "[Benoit Lelandais](mailto:benoit.lelandais@pasteur.fr)"
- name: "INCF test site"
id: "Dimiterpp"
url: "https://sites.imagej.net/Dimiterpp/"
description: >-
Update site for scale space filters and other INCF projects from GSOC
2014, 2015, 2016.
maintainers:
- "[Dimiter Prodanov](mailto:dimiterpp@gmail.com)"
- name: "IsletJ"
id: "IsletJ"
url: "https://sites.imagej.net/IsletJ/"
description: >-
Plugin for evaluation of microscopy images of Langerhans islets. Provides
estimate of area and count of islets, and an estimate of purity
(endocrine-to-exocrine tissue ratio).
maintainers:
- "[Jan Schier](mailto:schier@utia.cas.cz)"
- "[Jan Švihlík](mailto:Jan.Svihlik@vscht.cz)"
- name: "JAX Eye"
id: "MarkKrebs"
url: "https://sites.imagej.net/MarkKrebs/"
description: >-
Macro for processing brightfield fundus images of the mouse eye and
plugin for averaging replicate OCT volume scans.
maintainers:
- "[Mark Krebs](mailto:mark.krebs@jax.org)"
- name: "JOGL Canvas Deep Color / 3D"
id: "JOGLCanvas"
url: "https://sites.imagej.net/JOGLCanvas/"
description: >-
[JOGL Canvas](https://github.com/aschain/JOGL_Canvas_DC3D) is a plugin
for ImageJ1 that uses OpenGL and a graphics card to display images
rather than the ImageCanvas class, which is extended from java's canvas.
It replaces it with a [JOGL](https://jogamp.org/jogl/www/) OpenGL
GLCanvas instead. This allows 10-bit or greater color depth for
supported monitors and some modest 3D rendering.
maintainers:
- "[Aaron Schain](https://imagej.net/User:JOGLCanvas)"
- name: "Kappa"
id: "Kappa"
url: "https://sites.imagej.net/Kappa/"
description: >-
A Fiji plugin for Curvature Analysis.
maintainers:
- "[Hadrien Mary](https://imagej.net/User:Hadim)"
- name: "Lab-utility-plugins"
id: "Georgenm"
url: "https://sites.imagej.net/Georgenm/"
description: >-
A collection of plugins for file blinding, batch image conversion of
proprietary formats to tif, and other common helper functions.
Source and docs
[on GitHub](https://github.com/Macklin-Lab/imagej-microscopy-scripts).
maintainers:
- "[Nick George](mailto:nicholas.m.george@ucdenver.edu)"
- name: "Labkit"
id: "Labkit"
url: "https://sites.imagej.net/Labkit/"
description: >-
An advanced plugin for labeling and automatic segmentaion of Images.
maintainers:
- "[Matthias Arzt](mailto:arzt@mpi-cbg.de)"
- name: "LAG SIM"
id: "LagSIM"