Update render script and Makefile

terminal/biologicalimageanalysis

@@ -1,4 +1,4 @@
-                                                          Awesome Biological Image Analysis !Awesome (https://awesome.re/badge.svg) (https://awesome.re)
+                                                Awesome Biological Image Analysis !Awesome (https://awesome.re/badge.svg) (https://awesome.re)
 
 
   
@@ -58,20 +58,20 @@
 - DeepSlide (https://github.com/BMIRDS/deepslide) - A sliding window framework for classification of high resolution microscopy images.
 - EBImage (https://github.com/aoles/EBImage) - Image processing toolbox for R.
 - GPim (https://github.com/ziatdinovmax/GPim) - Gaussian processes and Bayesian optimization for images and hyperspectral data.
-- MAPS (https://github.com/mahmoodlab/MAPS) - MAPS (Machine learning for Analysis of Proteomics in Spatial biology) is a machine learning approach facilitating rapid and precise cell type identification with 
-human-level accuracy from spatial proteomics data.
-- MicroSAM (https://github.com/computational-cell-analytics/micro-sam) - Tools for segmentation and tracking in microscopy build on top of SegmentAnything. Segment and track objects in microscopy images 
-interactively.
+- MAPS (https://github.com/mahmoodlab/MAPS) - MAPS (Machine learning for Analysis of Proteomics in Spatial biology) is a machine learning approach facilitating rapid and precise cell type 
+identification with human-level accuracy from spatial proteomics data.
+- MicroSAM (https://github.com/computational-cell-analytics/micro-sam) - Tools for segmentation and tracking in microscopy build on top of SegmentAnything. Segment and track objects in 
+microscopy images interactively.
 - MorpholibJ (https://github.com/ijpb/MorphoLibJ) - Collection of mathematical morphology methods and plugins for ImageJ.
 - PartSeg (https://github.com/4DNucleome/PartSeg) - A GUI and a library for segmentation algorithms.
 - PyImSegm (https://github.com/Borda/pyImSegm) - Image segmentation - general superpixel segmentation and center detection and region growing.
-- Squidpy (https://github.com/scverse/squidpy) - Python framework that brings together tools from omics and image analysis to enable scalable description of spatial molecular data, such as transcriptome or 
-multivariate proteins.
+- Squidpy (https://github.com/scverse/squidpy) - Python framework that brings together tools from omics and image analysis to enable scalable description of spatial molecular data, such as 
+transcriptome or multivariate proteins.
 - StarDist (https://github.com/stardist/stardist) - Object detection with Star-convex shapes.
 - Suite2p (https://github.com/MouseLand/suite2p) - Pipeline for processing two-photon calcium imaging data.
 - SyMBac (https://github.com/georgeoshardo/SyMBac) - Accurate segmentation of bacterial microscope images using synthetically generated image data.
-- Trainable Weka Segmentation (https://github.com/fiji/Trainable_Segmentation) - Fiji plugin and library that combines a collection of machine learning algorithms with a set of selected image features to produce
-pixel-based segmentations.
+- Trainable Weka Segmentation (https://github.com/fiji/Trainable_Segmentation) - Fiji plugin and library that combines a collection of machine learning algorithms with a set of selected image
+features to produce pixel-based segmentations.
 
 Ecology
 - PAT-GEOM (http://ianzwchan.com/my-research/pat-geom/) - A software package for the analysis of animal colour pattern.
@@ -97,8 +97,8 @@
 - SNT (https://github.com/morphonets/SNT/) - ImageJ framework for semi-automated tracing and analysis of neurons.
 - TrailMap (https://github.com/AlbertPun/TRAILMAP/) - Software package to extract axonal data from cleared brains.
 - Wholebrain (https://github.com/tractatus/wholebrain) - Automated cell detection and registration of whole-brain images with plot of cell counts per region and Hemishpere.
-- ZVQ - Zebrafish Vascular Quantification (https://github.com/ElisabethKugler/ZFVascularQuantification) - Image analysis pipeline to perform 3D quantification of the total or regional zebrafish brain vasculature
-using the image analysis software Fiji.
+- ZVQ - Zebrafish Vascular Quantification (https://github.com/ElisabethKugler/ZFVascularQuantification) - Image analysis pipeline to perform 3D quantification of the total or regional 
+zebrafish brain vasculature using the image analysis software Fiji.
 
 
 
@@ -107,12 +107,14 @@
 - Aradeepopsis (https://github.com/Gregor-Mendel-Institute/aradeepopsis) - A versatile, fully open-source pipeline to extract phenotypic measurements from plant images.
 - DIRT (https://github.com/Computational-Plant-Science/DIRT) - Digital Imaging of Root Traits: Extract trait measurements from images of monocot and dicot roots.
 - LeafByte (https://zoegp.science/leafbyte) - Free and open source mobile app for measuring herbivory quickly and accurately.
-- PaCeQuant (https://mitobo.informatik.uni-halle.de/index.php/Applications/PaCeQuant) - An ImageJ-based tool which provides a fully automatic image analysis workflow for PC shape quantification.
+- PaCeQuant (https://mitobo.informatik.uni-halle.de/index.php/Applications/PaCeQuant) - An ImageJ-based tool which provides a fully automatic image analysis workflow for PC shape 
+quantification.
 - PhenotyperCV (https://github.com/jberry47/ddpsc_phenotypercv) - Header-only C++11 library using OpenCV for high-throughput image-based plant phenotyping.
 - PlantCV (https://github.com/danforthcenter/plantcv) - Open-source image analysis software package targeted for plant phenotyping.
 - PlantSeg (https://github.com/hci-unihd/plant-seg) - Tool for cell instance aware segmentation in densely packed 3D volumetric images.
 - RhizoTrak (https://prbio-hub.github.io/rhizoTrak/) - Open source tool for flexible and efficient manual annotation of complex time-series minirhizotron images.
-- Rhizovision Explorer (https://github.com/rootphenomicslab/RhizoVisionExplorer) - Free and open-source software developed for estimating root traits from images acquired from a flatbed scanner or camera.
+- Rhizovision Explorer (https://github.com/rootphenomicslab/RhizoVisionExplorer) - Free and open-source software developed for estimating root traits from images acquired from a flatbed 
+scanner or camera.
 - RootPainter (https://github.com/Abe404/root_painter) - Deep learning segmentation of biological images with corrective annotation.
 
 
@@ -120,7 +122,8 @@
 - Big-fish (https://github.com/fish-quant/big-fish) - Python package for the analysis of smFISH images.
 - DypFISH (https://github.com/cbib/dypfish) - Python library for spatial analysis of smFISH images.
 - RS-FISH (https://github.com/PreibischLab/RS-FISH) - Fiji plugin to detect FISH spots in 2D/3D images which scales to very large images.
-- Spotiflow (https://github.com/weigertlab/spotiflow) -  A deep learning-based, threshold-agnostic, and subpixel-accurate spot detection method developed for spatial transcriptomics workflows.
+- Spotiflow (https://github.com/weigertlab/spotiflow) -  A deep learning-based, threshold-agnostic, and subpixel-accurate spot detection method developed for spatial transcriptomics 
+workflows.
 - TissUUmaps (https://tissuumaps.github.io/) - Visualizer of NGS data, plot millions of points and interact, gate, export. ISS rounds and base visualization.
 
 
@@ -148,11 +151,11 @@
 - CellMigration (https://github.com/quantixed/CellMigration) - Analysis of 2D cell migration in Igor.
 - TrackMate (https://github.com/fiji/TrackMate) - User-friendly interface that allows for performing tracking, data visualization, editing results and track analysis in a convenient way.
 - TrackMateR (https://github.com/quantixed/TrackMateR) - R package to analyze cell migration and particle tracking experiments using outputs from TrackMate.
-- TracX (https://gitlab.com/csb.ethz/tracx) - MATLAB generic toolbox for cell tracking from various microscopy image modalities such as Bright-field (BF), phase contrast (PhC) or fluorescence (FL) with an 
-automated track quality assessment in
+- TracX (https://gitlab.com/csb.ethz/tracx) - MATLAB generic toolbox for cell tracking from various microscopy image modalities such as Bright-field (BF), phase contrast (PhC) or fluorescence
+(FL) with an automated track quality assessment in
 absence of a ground truth.
-- TraJClassifier (https://imagej.net/plugins/trajclassifier) - Fiji plugin that loads trajectories from TrackMate, characterizes them using TraJ and classifiies them into normal diffusion, subdiffusion, confined
-diffusion and directed/active motion by a random forest approach (through Renjin).
+- TraJClassifier (https://imagej.net/plugins/trajclassifier) - Fiji plugin that loads trajectories from TrackMate, characterizes them using TraJ and classifiies them into normal diffusion, 
+subdiffusion, confined diffusion and directed/active motion by a random forest approach (through Renjin).
 - QuimP (https://github.com/CellDynamics/QuimP) - Software for tracking cellular shape changes and dynamic distributions of fluorescent reporters at the cell membrane.
 - Usiigaci (https://github.com/oist/usiigaci) - Stain-free cell tracking in phase contrast microscopy enabled by supervised machine learning.
 
@@ -170,9 +173,12 @@
 - Fungal Feature Tracker (FFT) (https://github.com/hsueh-lab/FFT) - Tool to quantitatively characterize morphology and growth of filamentous fungi.
 
 Microbiology
-- BactMap (https://github.com/vrrenske/BactMAP) - A command-line based R package that allows researchers to transform cell segmentation and spot detection data generated by different programs into various plots.
-- BacStalk (https://drescherlab.org/data/bacstalk/docs/index.html) - Interactive and user-friendly image analysis software tool to investigate the cell biology of common used bacterial species.
-- BiofilmQ (https://drescherlab.org/data/biofilmQ/docs/) - Advanced biofilm analysis tool for quantifying the properties of cells inside large 3-dimensional biofilm communities in space and time.
+- BactMap (https://github.com/vrrenske/BactMAP) - A command-line based R package that allows researchers to transform cell segmentation and spot detection data generated by different programs
+into various plots.
+- BacStalk (https://drescherlab.org/data/bacstalk/docs/index.html) - Interactive and user-friendly image analysis software tool to investigate the cell biology of common used bacterial 
+species.
+- BiofilmQ (https://drescherlab.org/data/biofilmQ/docs/) - Advanced biofilm analysis tool for quantifying the properties of cells inside large 3-dimensional biofilm communities in space and 
+time.
 
 Yeast imaging
 - BABY (https://git.ecdf.ed.ac.uk/swain-lab/baby/) - An image processing pipeline for accurate single-cell growth estimation of
@@ -184,13 +190,13 @@
 
 Other
 - AICSImageIO (https://github.com/AllenCellModeling/aicsimageio) - Image reading, metadata conversion, and image writing for nicroscopy images in Python.
-- Biobeam (https://maweigert.github.io/biobeam) - Open source software package that is designed to provide fast methods for in-silico optical experiments with an emphasize on image formation in biological 
-tissues.
+- Biobeam (https://maweigert.github.io/biobeam) - Open source software package that is designed to provide fast methods for in-silico optical experiments with an emphasize on image formation 
+in biological tissues.
 - BoneJ (https://github.com/bonej-org/BoneJ2) - Collection of Fiji/ImageJ plug-ins for skeletal biology.
 - CaPTk (https://github.com/CBICA/CaPTk) - Cancer Imaging Phenomics Toolkit: A software platform to perform image analysis and predictive modeling tasks.
 - ColiCoords (https://github.com/Jhsmit/ColiCoords) - Python project for analysis of fluorescence microscopy data from rodlike cells.
-- CompactionAnalyzer (https://github.com/davidbhr/CompactionAnalyzer) - Python package to quantify the tissue compaction (as a measure of the contractile strength) generated by cells or multicellular spheroids 
-that are embedded in fiber materials.
+- CompactionAnalyzer (https://github.com/davidbhr/CompactionAnalyzer) - Python package to quantify the tissue compaction (as a measure of the contractile strength) generated by cells or 
+multicellular spheroids that are embedded in fiber materials.
 - Cytominer-database (https://github.com/cytomining/cytominer-database) - Command-line tools for organizing measurements extracted from images.
 - DetecDiv (https://github.com/gcharvin/DetecDiv) - Comprehensive set of tools to analyze time microscopy images using deep learning methods.
 - MIA (https://github.com/mianalysis/mia) - Fiji plugin which provides a modular framework for assembling image and object analysis workflows.
@@ -201,10 +207,11 @@
 - Nd2reader (https://github.com/Open-Science-Tools/nd2reader) - A pure-Python package that reads images produced by NIS Elements 4.0+.
 - OAD (https://github.com/zeiss-microscopy/OAD) - Collection of tools and scripts useful to automate microscopy workflows in ZEN Blue using Python and Open Application Development tools.
 - Pycytominer (https://github.com/cytomining/pycytominer) - Data processing functions for profiling perturbations.
-- Pyotf (https://github.com/david-hoffman/pyotf) - A simulation software package for modelling optical transfer functions (OTF)/point spread functions (PSF) of optical microscopes written in Python.
+- Pyotf (https://github.com/david-hoffman/pyotf) - A simulation software package for modelling optical transfer functions (OTF)/point spread functions (PSF) of optical microscopes written in 
+Python.
 - PyScratch (https://bitbucket.org/vladgaal/pyscratch_public.git/src) - Open source tool that autonomously performs quantitative analysis of in vitro scratch assays.
-- Quanfima (https://github.com/rshkarin/quanfima) - Quantitative Analysis of Fibrous Materials: A collection of useful functions for morphological analysis and visualization of 2D/3D data from various areas of 
-material science.
+- Quanfima (https://github.com/rshkarin/quanfima) - Quantitative Analysis of Fibrous Materials: A collection of useful functions for morphological analysis and visualization of 2D/3D data 
+from various areas of material science.
 - SimpleElastix (https://github.com/SuperElastix/SimpleElastix) - Multi-lingual medical image registration library.
 - Vaa3D (https://alleninstitute.org/what-we-do/brain-science/research/products-tools/vaa3d/) - Open-source software for 3D/4D/5D image visualization and analysis.
 - XitoSBML (https://github.com/spatialsimulator/XitoSBML) - ImageJ plugin which creates a Spatial SBML model from segmented images.
@@ -216,13 +223,14 @@
 
 Publications
 
-- A Hitchhiker's guide through the bio-image analysis software universe (https://febs.onlinelibrary.wiley.com/doi/10.1002/1873-3468.14451) - An article presenting a curated guide and glossary of bio-image 
-analysis terms and tools.
+- A Hitchhiker's guide through the bio-image analysis software universe (https://febs.onlinelibrary.wiley.com/doi/10.1002/1873-3468.14451) - An article presenting a curated guide and glossary
+of bio-image analysis terms and tools.
 - Biological imaging software tools (https://dx.doi.org/10.1038%2Fnmeth.2084) - The steps of biological image analysis and the appropriate tools for each step.
 - Data-analysis strategies for image-based cell profiling (https://doi.org/10.1038/nmeth.4397) - In-detail explanations of image analysis pipelines.
-- Large-scale image-based screening and profiling of cellular phenotypes (https://onlinelibrary.wiley.com/doi/10.1002/cyto.a.22909) - A workflow for phenotype extraction from high throughput imaging experiments.
-- Workflow and metrics for image quality control in large-scale high-content screens (https://linkinghub.elsevier.com/retrieve/pii/S2472555222075943) - Approaches for quality control in high-content imaging 
-screens.
+- Large-scale image-based screening and profiling of cellular phenotypes (https://onlinelibrary.wiley.com/doi/10.1002/cyto.a.22909) - A workflow for phenotype extraction from high throughput 
+imaging experiments.
+- Workflow and metrics for image quality control in large-scale high-content screens (https://linkinghub.elsevier.com/retrieve/pii/S2472555222075943) - Approaches for quality control in 
+high-content imaging screens.
 
 Footnotes
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