Ecosyste.ms: Packages
An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.
pypi.org "microscopy" keyword
bioio-ome-tiled-tiff 1.0.0
A BioIO reader plugin for reading tiled ome.tiff images.2 versions - Latest release: 6 months ago - 38 downloads last month - 0 stars on GitHub - 1 maintainer
jicbioimage.illustrate 0.6.1
Python package providing a set of tools for creating annotated images and illustrations.10 versions - Latest release: over 7 years ago - 3 dependent repositories - 20 downloads last month - 0 stars on GitHub - 1 maintainer
navigate-micro 0.0.5
Open source, smart, light-sheet microscopy control software.6 versions - Latest release: about 2 months ago - 162 downloads last month - 17 stars on GitHub - 1 maintainer
inpystem 0.1.1
A python library for STEM acquisition inpainting.5 versions - Latest release: about 4 years ago - 31 downloads last month - 4 stars on GitHub - 1 maintainer
nfinder 0.3
Automatic inference of neighboring cells based on their Delaunay triangulation.3 versions - Latest release: over 2 years ago - 1 dependent repositories - 19 downloads last month - 2 stars on GitHub - 1 maintainer
Top 6.3% on pypi.org
27 versions - Latest release: 4 months ago - 4 dependent packages - 2 dependent repositories - 1.25 thousand downloads last month - 145 stars on GitHub - 3 maintainers
pyxem 0.17.0
multi-dimensional diffraction microscopy27 versions - Latest release: 4 months ago - 4 dependent packages - 2 dependent repositories - 1.25 thousand downloads last month - 145 stars on GitHub - 3 maintainers
spiepy 0.2.1
SPIEPy (Scanning Probe Image Enchanter using Python) is a Python library to improve automatic pro...5 versions - Latest release: 6 months ago - 1 dependent repositories - 61 downloads last month - 1 maintainer
radiantkit 0.0.1
Radial Image Analysis Toolkit1 version - Latest release: over 5 years ago - 1 dependent repositories - 8 downloads last month - 2 stars on GitHub - 1 maintainer
magali 0.0.post13
Modelling and inversion of magnetic microscopy data1 version - Latest release: over 1 year ago - 12 downloads last month - 5 stars on GitHub - 1 maintainer
czitools 0.7.0
Tools to simplify reading CZI (Carl Zeiss Image) meta and pixel data26 versions - Latest release: 16 days ago - 368 downloads last month - 7 stars on GitHub - 1 maintainer
ffta 0.3.4
Fast Free Transient Analysis11 versions - Latest release: almost 3 years ago - 1 dependent repositories - 55 downloads last month - 3 stars on GitHub - 1 maintainer
Top 9.4% on pypi.org
86 versions - Latest release: 10 months ago - 2 dependent packages - 1 dependent repositories - 477 downloads last month - 250 stars on GitHub - 2 maintainers
pycroscopy 0.63.2
Python library for scientific analysis of microscopy data86 versions - Latest release: 10 months ago - 2 dependent packages - 1 dependent repositories - 477 downloads last month - 250 stars on GitHub - 2 maintainers
symbac 0.4.0
A package for generating synthetic images of bactera in phase contrast or fluorescence. Used for ...13 versions - Latest release: 3 months ago - 1 dependent repositories - 193 downloads last month - 17 stars on GitHub - 1 maintainer
bioio-sldy 1.0.1
A BioIO reader plugin for reading 3i slidebook (SLDY) images.4 versions - Latest release: 2 months ago - 119 downloads last month - 0 stars on GitHub - 2 maintainers
fpd-data-processing 0.2.1
Library for processing scanning transmission electron microscopy data acquired using a fast pixel...2 versions - Latest release: over 6 years ago - 1 dependent repositories - 20 downloads last month - 1 maintainer
brainatlas-api 0.0.2rc0
A lightweight python module to interact with atlases for systems neuroscience4 versions - Latest release: about 4 years ago - 1 dependent repositories - 34 downloads last month - 113 stars on GitHub - 3 maintainers
cellfinder 1.2.0
Automated 3D cell detection in large microscopy images98 versions - Latest release: 18 days ago - 3 dependent packages - 1.54 thousand downloads last month - 170 stars on GitHub - 2 maintainers
napari-psf-analysis 1.1.3
A plugin to analyse point spread functions (PSFs).16 versions - Latest release: about 1 month ago - 1 dependent repositories - 66 downloads last month - 7 stars on GitHub - 1 maintainer
frc 0.1.1
Library for computing Fourier Ring Correlation (FRC) curves and using them to determine image res...2 versions - Latest release: about 2 months ago - 1 dependent repositories - 45 downloads last month - 2 stars on GitHub - 1 maintainer
bioio-bioformats 1.0.0
A BioIO reader for reading bioformats formatted images.2 versions - Latest release: 6 months ago - 1 dependent package - 1.58 thousand downloads last month - 0 stars on GitHub - 1 maintainer
microjson 0.1.11
MicroJSON is a library for validating, parsing, and manipulating MicroJSON data.7 versions - Latest release: about 1 month ago - 46 downloads last month - 2 maintainers
scanpatterns 0.2.0
Parametric patterns for laser scanning microscopy4 versions - Latest release: about 2 years ago - 1 dependent repositories - 24 downloads last month - 1 stars on GitHub - 1 maintainer
microscopemetrics-omero 0.2.0
A package to compute metrics on OMERO images using micrsocope-metrics1 version - Latest release: 9 months ago - 9 downloads last month - 1 maintainer
instrumentools 0.1.3
Data processing and plotting scripts for chemistry workflows1 version - Latest release: over 3 years ago - 1 dependent repositories - 7 downloads last month - 3 stars on GitHub - 1 maintainer
fpd 0.2.5
FPD: Fast pixelated detector data storage, analysis and visualisation.20 versions - Latest release: about 2 years ago - 2 dependent repositories - 113 downloads last month - 9 stars on GitLab.com - 1 maintainer
multi-locus-analysis 0.1.0
Utilities for analyzing particle trajectories15 versions - Latest release: over 3 years ago - 1 dependent repositories - 35 downloads last month - 0 stars on GitHub - 1 maintainer
pyhmsa 0.2.0
Python implementation of the MSA / MAS / AMAS Hyper-Dimensional Data File specification10 versions - Latest release: about 5 years ago - 2 dependent repositories - 110 downloads last month - 2 stars on GitHub - 1 maintainer
microfpga 3.1.2
FPGA-based platform for the electronic control of microscopes.3 versions - Latest release: over 1 year ago - 19 downloads last month - 5 stars on GitHub - 1 maintainer
rosettasciio 0.4
Reading and writing scientific file formats4 versions - Latest release: about 2 months ago - 2 dependent packages - 1 dependent repositories - 13.9 thousand downloads last month - 44 stars on GitHub - 1 maintainer
pyhmsa-tiff 0.1.0
UNKNOWN1 version - Latest release: over 8 years ago - 1 dependent repositories - 10 downloads last month - 0 stars on GitHub - 1 maintainer
bmlab 0.8.0
Library for Brillouin microscopy data analysis37 versions - Latest release: over 1 year ago - 2 dependent packages - 2 dependent repositories - 329 downloads last month - 2 stars on GitHub - 2 maintainers
utoolbox-core 0.0.22
Core functions for uToolbox.49 versions - Latest release: almost 4 years ago - 2 dependent repositories - 154 downloads last month - 3 stars on GitHub - 1 maintainer
pylo 1.0.0
A python program to record image series with Lorentz-TEM.1 version - Latest release: about 3 years ago - 3 dependent repositories - 57 downloads last month - 1 stars on GitHub - 1 maintainer
deepflash2 0.2.3
A Deep learning pipeline for segmentation of fluorescent labels in microscopy images27 versions - Latest release: almost 1 year ago - 1 dependent package - 1 dependent repositories - 128 downloads last month - 57 stars on GitHub - 1 maintainer
palom 2024.4.1
Piecewise alignment for layers of mosaics21 versions - Latest release: about 1 month ago - 1 dependent package - 1 dependent repositories - 260 downloads last month - 16 stars on GitHub - 1 maintainer
pymontecarlo-casino2 1.1.0
Python interface for Monte Carlo simulation program Casino 23 versions - Latest release: over 2 years ago - 1 dependent repositories - 24 downloads last month - 20 stars on GitHub - 1 maintainer
pymontecarlo-gui 1.1.0
Python interface for Monte Carlo simulation programs2 versions - Latest release: over 2 years ago - 1 dependent repositories - 16 downloads last month - 20 stars on GitHub - 1 maintainer
pyminflux 0.4.1
Reader, processor, and viewer of MINFLUX raw data.8 versions - Latest release: 23 days ago - 101 downloads last month - 7 stars on GitHub - 1 maintainer
boss-ingest 0.12.0
Ingest client for the Boss17 versions - Latest release: about 3 years ago - 1 dependent repositories - 124 downloads last month - 5 stars on GitHub - 2 maintainers
ssm-analyze 0.2.6
Analysis GUI for scanning SQUID microscopy13 versions - Latest release: about 3 years ago - 1 dependent repositories - 46 downloads last month - 0 stars on GitHub - 1 maintainer
anasyspythontools 0.4.1
A suite of Python tools for use with Analysis Studio AFM-IR files.4 versions - Latest release: over 1 year ago - 32 downloads last month - 1 stars on GitHub - 1 maintainer
pathml 2.1.1
Tools for computational pathology15 versions - Latest release: about 1 year ago - 1 dependent repositories - 239 downloads last month - 367 stars on GitHub - 2 maintainers
Top 2.7% on pypi.org
31 versions - Latest release: 8 months ago - 13 dependent packages - 43 dependent repositories - 6.29 thousand downloads last month - 313 stars on GitHub - 4 maintainers
cucim 23.10.0
cuCIM - an extensible toolkit designed to provide GPU accelerated I/O, computer vision & image pr...31 versions - Latest release: 8 months ago - 13 dependent packages - 43 dependent repositories - 6.29 thousand downloads last month - 313 stars on GitHub - 4 maintainers
cucim-cu12 24.4.0
cuCIM - an extensible toolkit designed to provide GPU accelerated I/O, computer vision & image pr...3 versions - Latest release: about 2 months ago - 2 dependent packages - 3.09 thousand downloads last month - 313 stars on GitHub - 2 maintainers
cucim-cu11 24.4.0
cuCIM - an extensible toolkit designed to provide GPU accelerated I/O, computer vision & image pr...3 versions - Latest release: about 2 months ago - 131 downloads last month - 313 stars on GitHub - 2 maintainers
pyspacell 0.1.5
A Python package for single cell spatial image analysis6 versions - Latest release: over 4 years ago - 1 dependent repositories - 32 downloads last month - 18 stars on GitHub - 1 maintainer
nd2file 0.0.1.dev2
Access Nikon NIS-Elements ND2 files2 versions - Latest release: about 4 years ago - 2 dependent packages - 1 dependent repositories - 33 downloads last month - 0 stars on GitHub - 1 maintainer
acquifer 2.0.0
Utilitary functions when working with image datasets acquired with an ACQUIFER Imaging Machine mi...2 versions - Latest release: 3 months ago - 1 dependent package - 50 downloads last month - 0 stars on GitHub - 1 maintainer
roibuddy 1.0.1
GUI for editing segmentations when using SIMA3 versions - Latest release: over 7 years ago - 3 dependent repositories - 37 downloads last month - 3 maintainers
hyperspyui 1.3.1
Hyperspy Graphical User Interface14 versions - Latest release: about 1 year ago - 1 dependent repositories - 201 downloads last month - 25 stars on GitHub - 2 maintainers
exspy 0.2
EELS and EDS analysis with the HyperSpy framework2 versions - Latest release: about 2 months ago - 2 dependent packages - 1.52 thousand downloads last month - 8 stars on GitHub - 1 maintainer
holospy 0.1.1
Analysis of (off-axis) electron holography data with HyperSpy.4 versions - Latest release: 6 months ago - 1 dependent package - 500 downloads last month - 6 stars on GitHub - 1 maintainer
fpbase 0.0.1rc0
Stub for future FPbase API1 version - Latest release: 5 months ago - 7 downloads last month - 62 stars on GitHub - 1 maintainer
tttrlib 0.24.3
Read, write & process time-tagged time-resolved (TTTR) data.5 versions - Latest release: 4 months ago - 160 downloads last month - 18 stars on GitHub - 1 maintainer
blitzcurve 0.0.2
Time-resolved fluorescence anisotropy analysis.1 version - Latest release: about 6 years ago - 1 dependent repositories - 20 downloads last month - 0 stars on GitHub - 1 maintainer
qiber3d 0.7.0
Automated quantification of fibrous networks3 versions - Latest release: over 2 years ago - 1 dependent repositories - 31 downloads last month - 9 stars on GitHub - 1 maintainer
actk 0.2.2
Automated Cell Toolkit6 versions - Latest release: over 3 years ago - 45 downloads last month - 23 stars on GitHub - 1 maintainer
Top 9.8% on pypi.org
24 versions - Latest release: about 1 year ago - 3 dependent packages - 11 dependent repositories - 323 downloads last month - 19 stars on GitHub - 2 maintainers
intern 1.4.1
Python SDK for interacting with neuroscience data via the Boss API.24 versions - Latest release: about 1 year ago - 3 dependent packages - 11 dependent repositories - 323 downloads last month - 19 stars on GitHub - 2 maintainers
Top 5.6% on pypi.org
10 versions - Latest release: 4 months ago - 13 dependent packages - 4 dependent repositories - 2.07 thousand downloads last month - 113 stars on GitHub - 4 maintainers
bg-atlasapi 1.0.3
A lightweight python module to interact with atlases for systems neuroscience10 versions - Latest release: 4 months ago - 13 dependent packages - 4 dependent repositories - 2.07 thousand downloads last month - 113 stars on GitHub - 4 maintainers
strobopy 0.1.0
Analysis package for ultrafast stroboscopic TEM data1 version - Latest release: about 5 years ago - 1 dependent repositories - 10 downloads last month - 1 maintainer
fqmv
Fast quantification of morphological variation1 version
cellfinder-core 1.0.0
Automated 3D cell detection in large microscopy images32 versions - Latest release: 5 months ago - 4 dependent packages - 1 dependent repositories - 352 downloads last month - 19 stars on GitHub - 1 maintainer
pymontecarlo-penepma 1.0.0
Interface of Monte Carlo simulation program PENEPMA with pyMonteCarlo1 version - Latest release: over 2 years ago - 1 dependent repositories - 12 downloads last month - 20 stars on GitHub - 1 maintainer
biom3d 0.0.38
Biom3d. Framework for easy-to-use biomedical image segmentation.39 versions - Latest release: 2 months ago - 201 downloads last month - 17 stars on GitHub - 1 maintainer
pie 1.0.1
Colony recognition and growth measurement for microbial imaging2 versions - Latest release: over 1 year ago - 3 dependent repositories - 634 downloads last month - 4 stars on GitHub - 1 maintainer
gpim 0.3.9
Gaussian processes for image analysis14 versions - Latest release: about 3 years ago - 1 dependent repositories - 70 downloads last month - 55 stars on GitHub - 1 maintainer
naclib 1.1.0
Non-Affine Corrections on microscopy images using S/T Polynomial Decomposition5 versions - Latest release: about 1 year ago - 2 dependent repositories - 22 downloads last month - 0 stars on GitHub - 1 maintainer
pygpseq 3.4.1
A GPSeq image analysis package6 versions - Latest release: over 2 years ago - 1 dependent repositories - 31 downloads last month - 2 stars on GitHub - 1 maintainer
pyhmsa-matlab 0.1.0
UNKNOWN1 version - Latest release: over 8 years ago - 1 dependent repositories - 13 downloads last month - 0 stars on GitHub - 1 maintainer
tigerasi 0.0.26
a lightweight python driver for ASI brand Tiger Controllers21 versions - Latest release: 6 months ago - 157 downloads last month - 5 stars on GitHub - 1 maintainer
colicoords 0.1.5
Create a coordinate system in rod-shaped cells.5 versions - Latest release: over 4 years ago - 1 dependent package - 1 dependent repositories - 72 downloads last month - 24 stars on GitHub - 1 maintainer
cellocity 1.0.0
Velocity and vector analysis of microscopy data9 versions - Latest release: over 3 years ago - 1 dependent repositories - 45 downloads last month - 6 stars on GitHub - 1 maintainer
merlin-interface 0.0.5
Library for interfacing with the Merlin Medipix3 readout software over the TCP/IP API3 versions - Latest release: over 4 years ago - 1 dependent repositories - 28 downloads last month - 4 stars on GitLab.com - 1 maintainer
impose 0.4.8
Fit and superimpose shapes from different imaging modalities19 versions - Latest release: 16 days ago - 3 dependent repositories - 193 downloads last month - 1 stars on GitHub - 2 maintainers
segmentation 0.2.2
Mixture model segmentation6 versions - Latest release: about 3 years ago - 5 dependent repositories - 373 downloads last month - 1 stars on GitHub - 1 maintainer
basicpy 1.1.0
A python package for background and shading correction of optical microscopy images8 versions - Latest release: about 1 year ago - 2 dependent packages - 1 dependent repositories - 851 downloads last month - 53 stars on GitHub - 3 maintainers
bioimage 0.1.3
bioimage - library to make working with biomedical images more comfortable14 versions - Latest release: over 2 years ago - 1 dependent repositories - 72 downloads last month - 1 maintainer
Top 5.1% on pypi.org
29 versions - Latest release: about 3 years ago - 15 dependent packages - 35 dependent repositories - 4.83 thousand downloads last month - 43 stars on GitHub - 2 maintainers
nd2reader 3.3.0
A tool for reading ND2 files produced by NIS Elements29 versions - Latest release: about 3 years ago - 15 dependent packages - 35 dependent repositories - 4.83 thousand downloads last month - 43 stars on GitHub - 2 maintainers
Top 2.9% on pypi.org
41 versions - Latest release: about 1 month ago - 15 dependent packages - 11 dependent repositories - 10.6 thousand downloads last month - 45 stars on GitHub - 1 maintainer
nd2 0.10.1
Yet another nd2 (Nikon NIS Elements) file reader41 versions - Latest release: about 1 month ago - 15 dependent packages - 11 dependent repositories - 10.6 thousand downloads last month - 45 stars on GitHub - 1 maintainer
sitkibex 0.5.1
Image registration for iterative fluorescence microscopy3 versions - Latest release: 4 months ago - 122 downloads last month - 16 stars on GitHub - 2 maintainers
simtk 0.1.0
sim: structured illumination microscopy1 version - Latest release: over 3 years ago - 2 dependent repositories - 324 downloads last month - 4 stars on GitHub - 1 maintainer
cytoself 0.0.0
An image feature extractor with self-supervised learning5 versions - Latest release: about 3 years ago - 31 downloads last month - 69 stars on GitHub - 2 maintainers
jicbioimage.segment 0.4.0
Python package designed to make it easy to segment bio images.4 versions - Latest release: about 8 years ago - 3 dependent repositories - 19 downloads last month - 0 stars on GitHub - 1 maintainer
brainglobe-atlasapi 2.0.6
A lightweight python module to interact with and generate atlases for systems neuroscience.7 versions - Latest release: 18 days ago - 8 dependent packages - 5.38 thousand downloads last month - 113 stars on GitHub - 3 maintainers
empiar-depositor 1.6b30
Script for depositing the data into EMPIAR using EMPIAR API27 versions - Latest release: 10 months ago - 2 dependent repositories - 80 downloads last month - 6 stars on GitHub - 2 maintainers
jicbioimage 0.10.1
Python package designed to make it easy to work with bio images.4 versions - Latest release: over 8 years ago - 3 dependent repositories - 11 downloads last month - 3 stars on GitHub - 1 maintainer
clipper-python 0.1.1
Clipper libraries for experimental structural biology data3 versions - Latest release: about 6 years ago - 43 downloads last month - 2 maintainers
sxdm 1.0.0
Tools for analyzing Scanning X-ray Diffraction Microscopy data26 versions - Latest release: over 2 years ago - 1 dependent repositories - 363 downloads last month - 1 stars on GitHub - 1 maintainer
jicbioimage.transform 0.6.0
Python package wrapping commonly used image transformations.10 versions - Latest release: over 7 years ago - 4 dependent repositories - 29 downloads last month - 1 stars on GitHub - 1 maintainer
pixstem 0.4.0
Library for processing scanning transmission electron microscopy data acquired using a pixelated ...6 versions - Latest release: over 4 years ago - 1 dependent repositories - 69 downloads last month - 1 maintainer
nellie 0.1.8
Automated organelle segmentation, tracking, and hierarchical feature extraction in 2D/3D live-cel...9 versions - Latest release: about 1 month ago - 153 downloads last month - 26 stars on GitHub - 1 maintainer
temul-toolkit 0.1.7
Functions for analysis of high resolution electron microscopy and spectroscopy data.9 versions - Latest release: about 2 years ago - 1 dependent repositories - 184 downloads last month - 1 maintainer
napari-vesicles-segmentation 0.0.1
A simple plugin to detect vesicles in cells images.1 version - Latest release: almost 2 years ago - 25 downloads last month - 4 stars on GitHub - 1 maintainer
imagedataextractor 2.0.4
imagedataextractor is a Python library for electron microscopy image quantification.6 versions - Latest release: about 3 years ago - 1 dependent repositories - 54 downloads last month - 12 stars on GitHub - 2 maintainers
microscpsf-py 0.2
Gibson-Lanni PSF calculation code.2 versions - Latest release: over 3 years ago - 1 dependent repositories - 25 downloads last month - 34 stars on GitHub - 1 maintainer
axondeepseg 3.2.0
Python tool for automatic axon and myelin segmentation14 versions - Latest release: over 3 years ago - 55 downloads last month - 112 stars on GitHub - 3 maintainers
psfmodels 0.3.3
Scalar and vectorial models of the microscope point spread function (PSF).6 versions - Latest release: about 1 year ago - 1 dependent package - 1 dependent repositories - 689 downloads last month - 33 stars on GitHub - 1 maintainer
ngff-zarr 0.8.1
A lean and kind Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr impleme...24 versions - Latest release: 3 months ago - 2 dependent packages - 1 dependent repositories - 1.62 thousand downloads last month - 18 stars on GitHub - 1 maintainer
c7m 0.1.2
Module for analysis of high-throughput, fluorescence, wide-field microscopy images.3 versions - Latest release: almost 4 years ago - 1 dependent repositories - 35 downloads last month - 1 maintainer
cenfind 0.14.0
Score cells for centrioles in IF data32 versions - Latest release: 4 months ago - 159 downloads last month - 1 stars on GitHub - 1 maintainer
Related Keywords
python
54
image-processing
24
image-analysis
17
dask
16
scientific-formats
16
image-metadata
15
scientific-computing
15
segmentation
15
xarray
14
data analysis
14
bioio
13
imaging
13
neuroscience
13
electron-microscopy
12
STEM
11
brain
10
electron microscopy
10
hyperspy
9
registration
9
deep-learning
9
fluorescence
9
biology
9
electron
9
image
9
numpy
8
spectroscopy
8
analysis
8
image analysis
8
materials-science
7
microanalysis
7
TEM
7
multi-dimensional
7
napari
7
connectomics
6
x-ray-spectroscopy
6
scanning
6
microscopy-images
6
holography
6
microscope
6
atlases
5
hyperspectral
5
digital-pathology
5
machine-learning
5
data-analysis
5
quantitative-phase-imaging
5
quantitative phase imaging
5
digital holographic microscopy
5
database
5
EM
5
pytorch
5
hyperspy-extension
5
spatial
5
data-visualization
4
gui
4
cells
4
physical-sciences
4
medical-imaging
4
gpu
4
cuda
4
visualisation
4
fluorescence-microscopy-imaging
4
hmsa
4
file
4
format
4
calcium
4
x-ray
4
connectome
4
electron energy loss spectroscopy
4
tiff
4
scipy
4
SPM
4
cell
4
scientific
4
diffraction
4
deep learning
3
micro-manager
3
stitching
3
python3
3
eds
3
optics
3
refractive index
3
scattering
3
3d
3
hdf5
3
physics
3
psf
3
visualization
3
statistics
3
bioimage-analysis
3
probe
3
protein
3
deconvolution
3
monte-carlo-simulation
3
metadata
3
boss
3
napari-plugin
3
biomedical-image-processing
3
reconstruction
3
computer-vision
3
multidimensional
3