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
ssm-analyze 0.2.6
Analysis GUI for scanning SQUID microscopy13 versions - Latest release: about 3 years ago - 1 dependent repositories - 75 downloads last month - 0 stars on GitHub - 1 maintainer
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 - 52 downloads last month - 1 maintainer
sofima 0.1
Scalable Optical Flow-based Image Montaging and Alignment1 version - Latest release: about 2 years ago - 1 dependent repositories - 9 downloads last month - 47 stars on GitHub - 1 maintainer
smo 2.0.2
Implementation of the Silver Mountain Operator (SMO) for the estimation of background distributions.5 versions - Latest release: over 1 year ago - 1 dependent repositories - 79 downloads last month - 12 stars on GitHub - 1 maintainer
smlmvis 0.1.0
Superresolution visualization of 3D protein localization data from a range of microscopes6 versions - Latest release: 12 months ago - 1 dependent repositories - 34 downloads last month - 5 stars on GitHub - 1 maintainer
simtk 0.1.0
sim: structured illumination microscopy1 version - Latest release: over 3 years ago - 2 dependent repositories - 378 downloads last month - 4 stars on GitHub - 1 maintainer
Top 8.0% on pypi.org
18 versions - Latest release: over 7 years ago - 1 dependent package - 6 dependent repositories - 354 downloads last month - 3 maintainers
sima 1.3.2
Software for analysis of sequential imaging data18 versions - Latest release: over 7 years ago - 1 dependent package - 6 dependent repositories - 354 downloads last month - 3 maintainers
seq-io 0.10
Import .seq files into hyperspy4 versions - Latest release: almost 3 years ago - 1 dependent repositories - 21 downloads last month - 0 stars on GitHub - 1 maintainer
radiantkit 0.0.1
Radial Image Analysis Toolkit1 version - Latest release: over 5 years ago - 1 dependent repositories - 12 downloads last month - 2 stars on GitHub - 1 maintainer
qpsphere 0.5.9
library for analyzing spherical objects in phase imaging28 versions - Latest release: about 2 years ago - 2 dependent repositories - 310 downloads last month - 4 stars on GitHub - 2 maintainers
qpimage 0.9.2
library for manipulating quantitative phase images46 versions - Latest release: 7 months ago - 1 dependent package - 6 dependent repositories - 503 downloads last month - 0 stars on GitHub - 2 maintainers
qiber3d 0.7.0
Automated quantification of fibrous networks3 versions - Latest release: over 2 years ago - 1 dependent repositories - 42 downloads last month - 9 stars on GitHub - 1 maintainer
pyspacell 0.1.5
A Python package for single cell spatial image analysis6 versions - Latest release: over 4 years ago - 1 dependent repositories - 19 downloads last month - 18 stars on GitHub - 1 maintainer
pyrastitcher 0.0.1
Provides a Python interface to the Terastitcher program.1 version - Latest release: about 8 years ago - 2 dependent repositories - 10 downloads last month - 1 stars on GitHub - 1 maintainer
pyotf 0.0.3
A python library for simulating and analyzing microscope point spread functions (PSFs)3 versions - Latest release: over 1 year ago - 1 dependent package - 1 dependent repositories - 74 downloads last month - 67 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 - 32 downloads last month - 20 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
pymontecarlo-casino2 1.1.0
Python interface for Monte Carlo simulation program Casino 23 versions - Latest release: over 2 years ago - 1 dependent repositories - 35 downloads last month - 20 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
pyhmsa-matlab 0.1.0
UNKNOWN1 version - Latest release: over 8 years ago - 1 dependent repositories - 17 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 - 102 downloads last month - 2 stars on GitHub - 1 maintainer
pyhmsa-gui 0.1.5
Graphical components to represent HMSA specification5 versions - Latest release: over 8 years ago - 1 dependent repositories - 58 downloads last month - 0 stars on GitHub - 1 maintainer
pycellid 0.0.18
Functions to analyze single-cell2 versions - Latest release: over 2 years ago - 1 dependent repositories - 23 downloads last month - 1 stars on GitHub - 3 maintainers
pixstem 0.4.0
Library for processing scanning transmission electron microscopy data acquired using a pixelated ...6 versions - Latest release: about 4 years ago - 1 dependent repositories - 36 downloads last month - 1 maintainer
pie 1.0.1
Colony recognition and growth measurement for microbial imaging2 versions - Latest release: over 1 year ago - 3 dependent repositories - 563 downloads last month - 4 stars on GitHub - 1 maintainer
palom 2024.4.1
Piecewise alignment for layers of mosaics21 versions - Latest release: 20 days ago - 1 dependent package - 1 dependent repositories - 177 downloads last month - 16 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 - 17 downloads last month - 2 stars on GitHub - 1 maintainer
ndio 1.1.6
A Python library for open neuroscience data access and manipulation.53 versions - Latest release: over 7 years ago - 3 dependent repositories - 186 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 - 29 downloads last month - 0 stars on GitHub - 1 maintainer
napari-micromanager 0.1.0
Micro-Manager GUI interface in napari.7 versions - Latest release: 2 months ago - 1 dependent repositories - 93 downloads last month - 57 stars on GitHub - 1 maintainer
multi-locus-analysis 0.1.0
Utilities for analyzing particle trajectories15 versions - Latest release: about 3 years ago - 1 dependent repositories - 49 downloads last month - 0 stars on GitHub - 1 maintainer
minerva-lib 0.0.5
Minerva Python library4 versions - Latest release: over 3 years ago - 1 dependent repositories - 43 downloads last month - 2 stars on GitHub - 1 maintainer
microscpsf-py 0.2
Gibson-Lanni PSF calculation code.2 versions - Latest release: over 3 years ago - 1 dependent repositories - 21 downloads last month - 34 stars on GitHub - 1 maintainer
microimage 2.3.1
Python module to open common types of image used in microscopy.1 version - Latest release: about 3 years ago - 1 dependent repositories - 5 downloads last month - 0 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 - 24 downloads last month - 4 stars on GitLab.com - 1 maintainer
llspy 0.5.1
Lattice Light Sheet Processing Tools.2 versions - Latest release: about 2 months ago - 1 dependent repositories - 29 downloads last month - 25 stars on GitHub - 1 maintainer
jicimagelib 0.3.4
Python package designed to make it easy to work with microscopy images.6 versions - Latest release: over 8 years ago - 2 dependent repositories - 30 downloads last month - 0 stars on GitHub - 1 maintainer
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 - 17 downloads last month - 0 stars on GitHub - 1 maintainer
jicbioimage.core 0.15.0
Python package designed to make it easy to work with bio images.23 versions - Latest release: over 7 years ago - 7 dependent repositories - 59 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 - 25 downloads last month - 1 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 - 38 downloads last month - 0 stars on GitHub - 1 maintainer
jicbioimage 0.10.1
Python package designed to make it easy to work with bio images.4 versions - Latest release: about 8 years ago - 3 dependent repositories - 17 downloads last month - 3 stars on GitHub - 1 maintainer
instrumentools 0.1.3
Data processing and plotting scripts for chemistry workflows1 version - Latest release: over 3 years ago - 1 dependent repositories - 9 downloads last month - 3 stars on GitHub - 1 maintainer
inpystem 0.1.1
A python library for STEM acquisition inpainting.5 versions - Latest release: about 4 years ago - 54 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 - 55 downloads last month - 9 stars on GitHub - 2 maintainers
gpim 0.3.9
Gaussian processes for image analysis14 versions - Latest release: about 3 years ago - 1 dependent repositories - 103 downloads last month - 54 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 - 70 downloads last month - 1 stars on GitHub - 1 maintainer
fpd-live-imaging 0.0.4
Library for live processing and visualization of STEM data acquired using a fast pixelated detector1 version - Latest release: over 6 years ago - 1 dependent repositories - 20 downloads last month - 4 stars on GitLab.com - 1 maintainer
fpd-data-processing 0.2.1
Library for processing scanning transmission electron microscopy data acquired using a fast pixel...2 versions - Latest release: about 6 years ago - 1 dependent repositories - 20 downloads last month - 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 - 135 downloads last month - 9 stars on GitLab.com - 1 maintainer
ffta 0.3.4
Fast Free Transient Analysis11 versions - Latest release: almost 3 years ago - 1 dependent repositories - 90 downloads last month - 3 stars on GitHub - 1 maintainer
empiar-depositor 1.6b30
Script for depositing the data into EMPIAR using EMPIAR API27 versions - Latest release: 9 months ago - 2 dependent repositories - 126 downloads last month - 6 stars on GitHub - 2 maintainers
drymass 0.12.0
manipulation and analysis of phase microscopy data41 versions - Latest release: about 2 years ago - 1 dependent repositories - 307 downloads last month - 2 stars on GitHub - 2 maintainers
deepflash2 0.2.3
A Deep learning pipeline for segmentation of fluorescent labels in microscopy images27 versions - Latest release: 12 months ago - 1 dependent package - 1 dependent repositories - 258 downloads last month - 56 stars on GitHub - 1 maintainer
ddmtools 0.3.0
A Python library for doing differential dynamic microscopy on polydisperse samples7 versions - Latest release: about 2 years ago - 1 dependent repositories - 73 downloads last month - 1 stars on GitHub - 1 maintainer
clonedetective 0.0.3
A python package for the scalable analysis of fluorescent imaging data from lineage tracing exper...3 versions - Latest release: over 2 years ago - 1 dependent repositories - 32 downloads last month - 1 stars on GitHub - 1 maintainer
clipper-python 0.1.1
Clipper libraries for experimental structural biology data3 versions - Latest release: about 6 years ago - 62 downloads last month - 2 maintainers
bioio-sldy 1.0.1
A BioIO reader plugin for reading 3i slidebook (SLDY) images.4 versions - Latest release: about 2 months ago - 299 downloads last month - 0 stars on GitHub - 2 maintainers
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
cellocity 1.0.0
Velocity and vector analysis of microscopy data9 versions - Latest release: over 3 years ago - 1 dependent repositories - 54 downloads last month - 6 stars on GitHub - 1 maintainer
brainreg-napari 0.1.4
Multi-atlas whole-brain microscopy registration12 versions - Latest release: 5 months ago - 2 dependent packages - 140 downloads last month - 13 stars on GitHub - 1 maintainer
brainatlas-api 0.0.2rc0
A lightweight python module to interact with atlases for systems neuroscience4 versions - Latest release: almost 4 years ago - 1 dependent repositories - 32 downloads last month - 112 stars on GitHub - 3 maintainers
boss-ingest 0.12.0
Ingest client for the Boss17 versions - Latest release: about 3 years ago - 1 dependent repositories - 130 downloads last month - 5 stars on GitHub - 2 maintainers
blitzcurve 0.0.2
Time-resolved fluorescence anisotropy analysis.1 version - Latest release: almost 6 years ago - 1 dependent repositories - 24 downloads last month - 0 stars on GitHub - 1 maintainer
bioimage 0.1.3
bioimage - library to make working with biomedical images more comfortable14 versions - Latest release: over 2 years ago - 1 dependent repositories - 85 downloads last month - 1 maintainer
axondeepseg 3.2.0
Python tool for automatic axon and myelin segmentation14 versions - Latest release: over 3 years ago - 75 downloads last month - 112 stars on GitHub - 3 maintainers
mikro-napari 0.1.63
A napari plugin to interact with and provide functionality for a connected arkitekt server50 versions - Latest release: 4 months ago - 1 dependent repositories - 316 downloads last month - 0 stars on GitHub - 1 maintainer
nrefocus 0.5.3
numerical focusing (refocusing, autofocusing) of complex wave fields19 versions - Latest release: over 1 year ago - 2 dependent packages - 5 dependent repositories - 346 downloads last month - 7 stars on GitHub - 2 maintainers
pyapr 1.0.7
Content-adaptive image processing using the Adaptive Particle Representation11 versions - Latest release: 6 months ago - 2 dependent packages - 1 dependent repositories - 737 downloads last month - 14 stars on GitHub - 1 maintainer
Top 8.7% on pypi.org
20 versions - Latest release: 8 months ago - 4 dependent packages - 3 dependent repositories - 6.91 thousand downloads last month - 14 stars on GitHub - 1 maintainer
useq-schema 0.4.7
Schema for multi-dimensional microscopy experiments20 versions - Latest release: 8 months ago - 4 dependent packages - 3 dependent repositories - 6.91 thousand downloads last month - 14 stars on GitHub - 1 maintainer
napari-apr-viewer 1.0.1
A simple plugin to view APR images in napari6 versions - Latest release: 6 months ago - 1 dependent repositories - 59 downloads last month - 5 stars on GitHub - 1 maintainer
pma-python 2.0.0.177
Universal viewing of digital microscopy, whole slide imaging and digital pathology data108 versions - Latest release: 2 months ago - 1 dependent repositories - 439 downloads last month - 27 stars on GitHub - 2 maintainers
imagej-rolling-ball 2023.8.6
Python wrapper for ImageJ's rolling ball background subtraction using pyimagej7 versions - Latest release: 9 months ago - 40 downloads last month - 0 stars on GitHub - 1 maintainer
pycudadecon 0.4.1
Python wrapper for CUDA-accelerated 3D deconvolution3 versions - Latest release: 8 months ago - 1 dependent repositories - 49 downloads last month - 55 stars on GitHub - 1 maintainer
ndexchange 1.0.10
Python 3 program to download data from NeuroData11 versions - Latest release: about 5 years ago - 1 dependent repositories - 11 downloads last month - 4 stars on GitHub - 2 maintainers
mate-for-dummies 0.5.2
MATE for Dummies. Scienta Omicron MATE Scripting System in Python3 versions - Latest release: almost 4 years ago - 1 dependent repositories - 26 downloads last month - 1 maintainer
ashlar 1.18.0
Alignment by Simultaneous Harmonization of Layer/Adjacency Registration34 versions - Latest release: 4 months ago - 2 dependent repositories - 338 downloads last month - 111 stars on GitHub - 1 maintainer
qpformat 0.14.4
library for opening quantitative phase imaging data47 versions - Latest release: over 1 year ago - 1 dependent repositories - 392 downloads last month - 1 stars on GitHub - 2 maintainers
cytominer-database 0.3.4
A package for storing morphological profiling data.11 versions - Latest release: almost 3 years ago - 1 dependent package - 1 dependent repositories - 611 downloads last month - 9 stars on GitHub - 5 maintainers
cell-tracking-bc 2024.1 💰
Base Classes for Cell Tracking in Microscopy89 versions - Latest release: 4 months ago - 739 downloads last month - 6,321 stars on GitHub - 1 maintainer
bioio-base 1.0.0
Typing, base classes, and more for BioIO projects.6 versions - Latest release: 5 months ago - 13 dependent packages - 1 dependent repositories - 6.31 thousand downloads last month - 0 stars on GitHub - 2 maintainers
pco 2.1.2
This class provides methods for using pco cameras.10 versions - Latest release: 3 months ago - 1 dependent package - 1 dependent repositories - 499 downloads last month - 1 maintainer
napari-psf-analysis 1.1.3
A plugin to analyse point spread functions (PSFs).16 versions - Latest release: 20 days ago - 1 dependent repositories - 147 downloads last month - 7 stars on GitHub - 1 maintainer
Top 9.4% on pypi.org
86 versions - Latest release: 9 months ago - 2 dependent packages - 1 dependent repositories - 423 downloads last month - 250 stars on GitHub - 2 maintainers
pycroscopy 0.63.2
Python library for scientific analysis of microscopy data86 versions - Latest release: 9 months ago - 2 dependent packages - 1 dependent repositories - 423 downloads last month - 250 stars on GitHub - 2 maintainers
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 - 42 downloads last month - 1 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 - 350 downloads last month - 2 stars on GitHub - 2 maintainers
roibuddy 1.0.1
GUI for editing segmentations when using SIMA3 versions - Latest release: over 7 years ago - 3 dependent repositories - 33 downloads last month - 3 maintainers
Top 9.8% on pypi.org
24 versions - Latest release: about 1 year ago - 3 dependent packages - 11 dependent repositories - 213 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 - 213 downloads last month - 19 stars on GitHub - 2 maintainers
biom3d 0.0.38
Biom3d. Framework for easy-to-use biomedical image segmentation.39 versions - Latest release: about 2 months ago - 713 downloads last month - 17 stars on GitHub - 1 maintainer
actk 0.2.2
Automated Cell Toolkit6 versions - Latest release: over 3 years ago - 75 downloads last month - 23 stars on GitHub - 1 maintainer
scanpatterns 0.2.0
Parametric patterns for laser scanning microscopy4 versions - Latest release: about 2 years ago - 1 dependent repositories - 29 downloads last month - 1 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 - 20 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 - 26 downloads last month - 2 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 - 79 downloads last month - 24 stars on GitHub - 1 maintainer
segmentation 0.2.2
Mixture model segmentation6 versions - Latest release: about 3 years ago - 5 dependent repositories - 374 downloads last month - 1 stars on GitHub - 1 maintainer
cytoself 0.0.0
An image feature extractor with self-supervised learning5 versions - Latest release: about 3 years ago - 71 downloads last month - 67 stars on GitHub - 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 - 73 downloads last month - 1 stars on GitHub - 1 maintainer
optical-flow-registration-bioinfotongli 1.0.0 removed
Optical-flow-based image registration for fluorescence microscopy images1 version - Latest release: about 2 years ago - 1 dependent repositories - 7 downloads last month - 3 stars on GitHub - 1 maintainer
feature-based-registration-bioinfotongli 2.0.1 removed
Feature-spot-based image registration for fluorescence microscopy images2 versions - Latest release: about 2 years ago - 1 dependent repositories - 7 downloads last month - 3 stars on GitHub - 1 maintainer
staged-image-recovery 0.0.1 removed
Recover images from proximity information.1 version - Latest release: over 1 year ago - 1 maintainer
Related Keywords
python
54
image-processing
24
dask
16
scientific-formats
16
image-analysis
16
image-metadata
15
scientific-computing
15
segmentation
15
data analysis
14
xarray
14
neuroscience
13
imaging
13
bioio
13
electron-microscopy
12
STEM
11
electron microscopy
10
brain
10
deep-learning
9
fluorescence
9
hyperspy
9
electron
9
registration
9
image
9
biology
9
image analysis
8
numpy
8
spectroscopy
8
analysis
8
TEM
7
materials-science
7
multi-dimensional
7
napari
7
microanalysis
7
holography
6
connectomics
6
x-ray-spectroscopy
6
microscope
6
scanning
6
microscopy-images
6
hyperspy-extension
5
atlases
5
hyperspectral
5
data-analysis
5
machine-learning
5
quantitative phase imaging
5
database
5
digital holographic microscopy
5
pytorch
5
EM
5
digital-pathology
5
quantitative-phase-imaging
5
spatial
5
format
4
hmsa
4
tiff
4
x-ray
4
cells
4
medical-imaging
4
gpu
4
cuda
4
visualisation
4
physical-sciences
4
data-visualization
4
scientific
4
cell
4
fluorescence-microscopy-imaging
4
electron energy loss spectroscopy
4
gui
4
scipy
4
connectome
4
calcium
4
diffraction
4
SPM
4
file
4
EELS
3
protein
3
optics
3
deep learning
3
probe
3
scattering
3
refractive index
3
eels
3
reconstruction
3
deconvolution
3
boss
3
python3
3
multidimensional
3
napari-plugin
3
visualization
3
nis-elements
3
nikon
3
nd2
3
micro-manager
3
statistics
3
monte-carlo-simulation
3
bioimage-analysis
3
metadata
3
nvidia
3
multidimensional-image-processing
3
3d
3