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listing content
Name	Category	requires	Type	interaction level	License/Openness	has function	has topic
MountainsMap	Software	Segmentation of Clustered Cells in MATLAB, Spot Detection (KNIME), MountainsMap	Collection	Automated	Commercial
Mouse embryos	Dataset
Movies of drosophila epithelia development, with manually annotated extrusions and divisions - From DeXtrusion publication	Dataset
Movies of mouse oocyte maturation in transmitted light	Dataset
Moving Least Squares	Software	ImageJ	Component	Automated	I do not know
MRI Simulation and Reconstruction	Software	MATLAB	Collection	Manual	Free and open source	Image reconstruction, Synthetic image generation	Bioimage informatics, Magnetic resonance imaging
MSRC Registration Toolbox	Software		Component	Automated, Semi-automated	Free and open source	Image registration, Feature-based registration	Fluorescence microscopy, Multimodal imaging
MTrack2 (ImageJ)	Software	ImageJ	Component	Semi-automated	Free and open source	Isolated object tracking	Bioimage informatics
MTrackJ	Software	ImageJ, ImageScience.jar	Component	Automated	Free and open source	Object tracking
Multi Kymograph	Software	ImageJ	Collection	Semi-automated	Free and open source	Object tracking, Trajectory analysis	Bioimage informatics
Multi Otsu Threshold	Software	ImageJ, KNIME Multilevel Thresholding, Histogram	Component	Semi-automated	Free and open source	Image thresholding	Bioimage informatics
Multi-Template matching	Software	Fiji	Component	Semi-automated	Free and open source	Object detection, Pattern recognition	Bioimage informatics, High content screening
Multi-touch gestures	Software	Icy Multi-Touch provider	Component	Automated	Free and open source	Data handling
Multiple Image Processor	Software	ImageJ, Fiji	Component	Semi-automated	Free and open source, I do not know
MultiStackReg	Software	Fiji, TurboReg	Component	Automated	Free and open source	Alignment construction, Image registration	Imaging, Electron microscopy, Light microscopy
Multithreaded Image Processing	Software	ImageJ	Component	Automated	Free and open source	Data handling	Bioimage informatics
Multithreaded Image Processing in Javascript	Software	ImageJ	Component	Automated	Free and open source	Data handling
MultiThresholder (ImageJ)	Software	ImageJ	Component	Semi-automated	Free and open source	Image thresholding	Bioimage informatics
Multiview Reconstruction	Software	BigDataViewer, ImageJ, ImgLib2	Collection	Manual, Semi-automated	Free and open source	Image registration, Affine registration, Rigid registration, Affine transformation, Chromatic aberration correction, Drift correction, Image deconvolution, Selective plane illumination microscopy reconstruction, Visualisation	Light-sheet microscopy
muscle cross-sections	Dataset

Operation
-Alignment construction
--Image registration
---Affine registration
----Rigid registration
---Deformable registration
---Feature-based registration
-Analysis
--Frequency analysis
--Image analysis
---Colocalisation analysis
----Object-based colocalisation
----Pixel-based colocalisation
---Filament tracing
---Image classification
---Image feature detection
----Edge detection
----Spot detection
---Image segmentation
----Adaptative thresholding
----Cell segmentation
----Image thresholding
----Interactive segmentation
----Local thresholding
----Model-based segmentation
-----Active contours
----Pixel classification
----Region growing
----Watershed segmentation
---Neuron image analysis
---Object classification
---Object counting
---Object detection
----Single molecule localisation
---Object feature extraction
----Homogeneity
----Shape features
----Texture extraction
---Object tracking
----Collective object tracking
----Isolated object tracking
-----Cell tracking
-----Particle tracking
----Trajectory analysis
----Wound-healing analysis
---Optical flow analysis
-Annotation
--Image annotation
---Landmark assignment
-Classification
--Image classification
--Object classification
--Pixel classification
-Clustering
-Data handling
--Conversion
--Editing
-Generation
--Image generation
---Image reconstruction
----Image deconvolution
----Image denoising
----Image projection
----Image stitching
----Selective plane illumination microscopy reconstruction
----Single molecule localisation
----Structured illumination reconstruction
----Tomographic reconstruction
---Synthetic image generation
-Image processing
--Frequency analysis
--Geometrical transformation
---Affine transformation
----Linear transformation
----Rotation
---Warping
--Image convolution
--Image correction
---Chromatic aberration correction
---Detector bias correction
---Detector gain correction
---Drift correction
---Geometric distortion correction
---Illumination correction
---Spectral unmixing
--Image crop
--Image enhancement
---Contrast enhancement
---Feature enhancement
---Image denoising
---Smoothing
--Image reconstruction
---Image deconvolution
---Image denoising
---Image projection
---Image stitching
---Selective plane illumination microscopy reconstruction
---Single molecule localisation
---Structured illumination reconstruction
---Tomographic reconstruction
--Image registration
---Affine registration
----Rigid registration
---Deformable registration
---Feature-based registration
--Image segmentation
---Adaptative thresholding
---Cell segmentation
---Image thresholding
---Interactive segmentation
---Local thresholding
---Model-based segmentation
----Active contours
---Pixel classification
---Region growing
---Watershed segmentation
--Morphological operation
---Closing
---Dilation
---Distance transform
---Erosion
---Opening
---Skeletonisation
---Top-hat transform
-Optimisation or refinement
--Parameter optimisation
-Prediction and recognition
--Pattern recognition
-Validation
--Image validation
-Visualisation
--Image visualisation
---Anaglyph
---Montage
---Overlay
---Slice rendering
---Surface rendering
---Volume rendering
--Plotting

Topic
-Bioimage informatics
-Data sharing
-Digital histology
-High content screening
-Imaging
--Bioluminescence imaging
--Fixed sample imaging
--Live sample imaging
---Ex-vivo imaging
---In-vitro imaging
---In-vivo imaging
--Magnetic resonance imaging
--Microscopy
---Correlative Light and Electron Microscopy
---Electron microscopy
----Scanning electron microscopy
-----Cryo scanning electron microscopy
-----Focused ion beam scanning electron microscopy
-----Serial block-face scanning electron microscopy
----Transmission electron microscopy
-----Electron tomography
------Cryo electron tomography
-----Scanning transmission electron microscopy
---Light microscopy
----Area-capturing microscopy
-----Light-sheet microscopy
-----Widefield microscopy
----Fluorescence microscopy
-----Confocal fluorescence microscopy
-----Fluctuation based microscopy
-----Fluorescence correlative spectroscopy
-----Fluorescence lifetime imaging microscopy
-----Fluorescence recovery after photobleaching
-----Förster resonance energy transfer
-----Image correlation spectroscopy
-----Super-resolution microscopy
------Single molecule localization microscopy
------Stimulated Emission Depletion microscopy
------Structured illumination microscopy
----Point-scanning microscopy
-----Confocal microscopy
------Confocal fluorescence microscopy
-----Light-sheet microscopy
-----Multi-photon microscopy
----Transmission light microscopy
-----Bright field microscopy
-----Dark field microscopy
-----DIC microscopy
-----Phase contrast microscopy
-----Polarized light microscopy
----Widefield microscopy
--Multimodal imaging
--Spectroscopy
---Fluorescence correlative spectroscopy
---Nuclear magnetic resonance spectroscopy
--Tomography
---Computerized tomography
---Photoacoustic tomography
---Positron emission tomography
---Single-photon emission computed tomography
--Ultrasonography
-In-silico reconstruction
-Machine learning
--Reinforcement learning
--Supervised learning
--Unsupervised learning
-Sample
-Sample preparation
--Critical-point drying
--Cryo fixation
---High-pressure freezing
---Plunge freezing
--Freeze fracturing
-Statistics

2D Gaussian Fitting
Actin
actomyosin
adenocarcinoma
adipocyte
adipose tissue cellularity
Alzheimer's disease
amoeboid cells
angiogenesis
ants
Arabidopsis ovules
Arabidopsis thaliana
Arabidopsis thaliana seedlings
Artemia
arterioles
Astrocytes
axon
bacteria
bacterial colonies
bead
blood cells
blood vessels
bones
brain
branching
breast cancer
brownian motion
c. elegans
C.elegans embryo development
Ca2+
Caenorhabditis elegans
calcium signalling
calcium sparks
cancer
Capillaries
cardiomyocytes
cell area
cell biology
cell membrane
cell migration
cell motility
cell organelles
cell protrusion
cell retraction
cell tracking
cell volume
cells
central nervous system
centriole
centromere
chromatin
clathrin
clustered cells
collagen
connectomics
COVID
cytoo
cytoplasm
cytoskeleton
dendrites
Dendritic Spine
developmental biology
Dictyostelium
diffusion
division
DNA damage
dragonfly neuron
drosophila
Drosophila melanogaster
drosophila wing
E-Cadherin
E. coli
EB1
embryo
endoplasmic reticulum
endosomes
endosomes (4656
eosin
Epidermis
epithelia
evolution
Exocytosis
exosomes
extrusion
fiber
fibronectin
filament
filopodia
flow
fluid
Fluorece
Focal Adhesion
foci
fruit fly neuron
fungi
ganglion
gel analysis
gene foci
gene loci
gland
glioblastoma
Golgi apparatus
grayscale image
growth
H&E staining
heart
Hela cells
hematoxylin
Hippocampal Neurons
histopathology
HL60 cells
human induced pluripotent stem cell
human oocyte
immune system
interdigitation measurements
invagination
invasive breast carcinoma cells
invasive cell migration
Ki67
kidney tubules
kinetochore
Label free
lamellipodia
larva
Leaf
leaf infection
ligand-receptor
lipid droplets
localization of anatomical structures
lung
lung airways
Lymphatic Vessel Density
lysosome
macrophage
Mammary Epithelial
Maturation
medaka
Meiosis
membrane
membrane dynamics
mi
Mice
MicroArray
microbe
Microglia
microtubules
minerals
mitochondria
mitosis
molecule
morphological phenotype
mosaic
mouse
mouse brain
mRNA
Muscle
muscle fiber orientation
Muscle Stem Cells
myelin
myofibres
myosin
nanoparticles
ndpi
neocortical axons
network
neurite arbor
neurite area
neurite attachment points
neurite endpoints
neurite length
neurite outgrowth measurement
neurites
neuroanatomy
neuroblastoma
neuromuscular axons
neuron
neuronal arbors
neurons
NIH-3T3
Nucelus
Nuclear pores
nuclei
nucleus
olfactory axons
olfactory fibre
olfactory projection fibres
oligodendrocyte
Oligodendrocytes
Oligodendrocytes, Oligodendrocytes differentiation, Morphological Analysis
Oocyte
organoid
ovarian cancer
particles
pathology
Phagocytosis
Physiology
plant
plant virurs
plant virus, leaf infection
plate number
Pressure myography
progesterone receptor
proteins
pulmonary airways
REF-52 cells
retina
RNAFish
RNAi
rod-shaped
root
sea urchin oocyte
sensory organ precusor
single molecule
skeleton
skin
smFish
Spatial omics
Spatial transcriptomics
spheroid
spindle elongation
spots
stationary noise
stem cells
stereo logy
subcellular compartments
subcellular interactions
subcellular structure
synapse
textiles
thickness measurements
tiled images
tiles
tissue
tissue engineering
tissues
toxicology
Trabeculae
Track Editing
trafficking
transcripts
transfected
tubular network
tubular structure
tubulin
tumor
vesicle
vesicles
Vimentin
viral particles
Virus
well number
worm
wound closure
yeast
yeast Schizosaccharomyces pombe
zebrafish
zyxin