link dump

8 files changed, 189 insertions, 4 deletions

diff --git a/posts/daq.md b/posts/daq.md
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+title: data acquisition hardware
+date: 2020-04-12
+
+This post is a roundup of data acquisition hardware that I want to keep track of.
+This includes both analog-to-digital, digital-to-analog, and multifunction.
+
+# table of contents
+
+[TOC]
+
+# multifunction
+
+## GaGe
+
+[website](http://www.gage-applied.com/)
+
+GaGe, established in 1987, is a customer-oriented worldwide industry leader in advanced instrumentation based on the personal computer platform.
+GaGe designs and develops hardware and software for the Test and Measurement, Embedded Data Acquisition and Automated Test market segments.
+Our product offering includes PCIe, PCI and USB digitizers, modular instruments, turnkey measurement systems, PC oscilloscope software and supporting software development kits (SDKs).
+
+## LabJack
+
+[website](https://labjack.com/)
+
+LabJack makes USB, Ethernet, and WiFi based measurement and automation devices which provide analog and digital inputs and outputs.
diff --git a/posts/data-processing.md b/posts/data-processing.md
index 9d04a14..3f74b7b 100644
--- a/posts/data-processing.md
+++ b/posts/data-processing.md
@@ -1,5 +1,5 @@
 title: data processing
-date: 2020-04-12
+date: 2020-05-23
 
 This post is a roundup of open source scientific data processing projects that I know of.
 I've organized them alphabetically.
@@ -10,8 +10,46 @@ Obviously this only scratches the surface, but I've tried to put in just the one
 
 [TOC]
 
-# Skultrafast
+# [GCPy](https://github.com/geoschem/gcpy)
 
-[source](https://github.com/Tillsten/skultrafast)
+GCPy is a Python-based toolkit containing useful functions for working specifically with the GEOS-Chem model of atmospheric chemistry and composition.
+
+GCPy aims to build on the well-established scientific Python technical stack, leveraging tools like cartopy and xarray to simplify the task of working with model output and performing atmospheric chemistry analyses.
+
+# KOALA
+
+[website](http://www.bristoldynamics.com/resources/)
+
+[publication](https://doi.org/10.1063/1.4884516)
+
+Here, we present a new program for decomposing mixed transient spectra into their individual component spectra and extracting the corresponding kinetic traces: KOALA (Kinetics Observed After Light Absorption).
+The software combines spectral target analysis with brute-force linear least squares fitting, which is computationally efficient because of the small nonlinear parameter space of most spectral features.
+
+# pycroscopy
+
+[website](https://pycroscopy.github.io/pycroscopy/about.html)
+
+[source](https://github.com/pycroscopy/pycroscopy)
+
+pycroscopy is a python package for image processing and scientific analysis of imaging modalities such as multi-frequency scanning probe microscopy, scanning tunneling spectroscopy, x-ray diffraction microscopy, and transmission electron microscopy.
+pycroscopy uses a data-centric model wherein the raw data collected from the microscope, results from analysis and processing routines are all written to standardized hierarchical data format (HDF5) files for traceability, reproducibility, and provenance.
+
+# PyTrA
+
+[website](https://sourceforge.net/projects/pytra/)
+
+[source](https://github.com/nzjakemartin/PyTrA)
+
+Analysis of ultra-fast transient absorption spectra.
+
+# pyUSID
+
+[website](https://pycroscopy.github.io/pyUSID/about.html)
+
+Python framework for storing, visualizing, and processing spectroscopy, imaging or any observational / experimental data.
+
+The Universal Spectroscopic and Imaging Data (USID) model.
+
+# [Skultrafast](https://github.com/Tillsten/skultrafast)
 
 Skultrafast stands for scikit.ultrafast and is an python package which aims to include everything needed to analyze data from time-resolved spectroscopy experiments in the femtosecond domain.
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diff --git a/posts/gui.md b/posts/gui.md
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+title: graphical user interface
+date: 2020-05-23
+
+This is a roundup post of links to graphical user interface projects that I find relevant.
+
+# table of contents
+
+[TOC]
+
+# qt
+
+## [PyDM](http://slaclab.github.io/pydm/index.html)
+
+PyDM is a PyQt-based framework for building user interfaces for control systems.
+
+The goal is to provide a no-code, drag-and-drop system to make simple screens, as well as a straightforward python framework to build complex applications.
+
+# web technologies
+
+## [Graphana](https://grafana.com/)
+
+Grafana allows you to query, visualize, alert on and understand your metrics no matter where they are stored. Create, explore, and share dashboards with your team and foster a data driven culture.
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diff --git a/posts/instrumental-software.md b/posts/instrumental-software.md
index 610d815..ba7684e 100644
--- a/posts/instrumental-software.md
+++ b/posts/instrumental-software.md
@@ -1,5 +1,5 @@
 title: instrumental-software
-date: 2020-04-12
+date: 2020-05-23
 
 This post is a roundup of open source instrumental software projects that I know of.
 I've organized them alphabetically.
@@ -50,6 +50,13 @@ Instrumental is a Python-based library for controlling lab hardware like cameras
 
 Simple yet powerful instrumentation in Python
 
+# micro-manager
+
+[website](https://micro-manager.org/)
+
+A really cool project.
+Check out the [whitepaper](https://github.com/nicost/uScopeControl/blob/master/Software%20for%20Microscopy%20Workshop%20WhitePaper.pdf) and their [CMMCore Class Reference](https://valelab4.ucsf.edu/~MM/doc/MMCore/html/class_c_m_m_core.html).
+
 # PyCMDS
 
 (personal project)
@@ -62,6 +69,13 @@ Python display manager.
 PyDM is a PyQt-based framework for building user interfaces for control systems.
 The goal is to provide a no-code, drag-and-drop system to make simple screens, as well as a straightforward python framework to build complex applications.
 
+# Py-Hardware-Support
+
+[website](https://ddietze.github.io/Py-Hardware-Support/index.html)
+
+Here’s a small collection of some python modules that can be used to add hardware support to your programs.
+I have written those to be easy to use but not necessarily covering all the functionality the library or device has to offer.
+
 # python-microscopy
 
 [website](http://www.python-microscopy.org/)
@@ -82,6 +96,12 @@ python-microscopy is a large package including a farily mature microscope contro
 Quote:
 A Python platform for controlling custom laboratory experiments and visualizing scientific data.
 
+# SFGacquisition
+
+[source](https://github.com/GeigerGroup/SFGacquisition)
+
+Software for interfacing with WinSpec/Lightfield and WinTOPAS as well as Thorlabs motorized optic mounts to control SFG spectral acquisitions at multiple DFG positions.
+
 # storm-control
 
 [source](https://github.com/ZhuangLab/storm-control)
diff --git a/posts/open-hardware.md b/posts/open-hardware.md
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+title: open hardware
+date: 2020-05-23
+
+This post is a roundup of open source hardware projects that I find relevant.
+
+# table of contents
+
+[TOC]
+
+# NanoJ-Fluidics
+
+[wiki](https://github.com/HenriquesLab/NanoJ-Fluidics/wiki)
+
+[source](https://github.com/HenriquesLab/NanoJ-Fluidics)
+
+[publication](https://www.nature.com/articles/s41467-019-09231-9)
+
+Combining and multiplexing microscopy approaches is crucial to understand cellular events, but requires elaborate workflows.
+Here, we present a robust, open-source approach for treating, labelling and imaging live or fixed cells in automated sequences.
+NanoJ-Fluidics is based on low-cost Lego hardware controlled by ImageJ-based software, making high-content, multimodal imaging easy to implement on any microscope with high reproducibility.
+We demonstrate its capacity on event-driven, super-resolved live-to-fixed and multiplexed STORM/DNA-PAINT experiments.
+
+# opentrons
+
+[website](https://opentrons.com/)
diff --git a/posts/optics.md b/posts/optics.md
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+title: optics companies
+date: 2020-05-23
+
+This post is a roundup of interesting optics companies.
+
+# table of contents
+
+[TOC]
+
+# standa
+
+[website](http://www.standa.lt/)
+
+Focused on opto-mechanical.
diff --git a/posts/pcb-printing.md b/posts/pcb-printing.md
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+title: pcb printing
+date: 2020-05-23
+
+This post is currently a roundup of PCB printers.
+Perhaps in the future it could become my notes about how to print PCBs.
+
+# table of contents
+
+[TOC]
+
+# elecrow
+
+[website](https://www.elecrow.com/pcb-manufacturing.html)
+
+# JLCPCB
+
+[website](https://jlcpcb.com/)
+
+# OSH Park
+
+[website](https://oshpark.com/)
+
+# PCBWay
+
+[website](https://www.pcbway.com/)
diff --git a/posts/plotting.md b/posts/plotting.md
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+++ b/posts/plotting.md
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+title: plotting scientific data
+date: 2020-05-23
+
+This post is a roundup of interesting ideas about plotting scientific data.
+
+# table of contents
+
+[TOC]
+
+# CMasher
+
+[website](https://cmasher.readthedocs.io/index.html)
+
+[source](https://github.com/1313e/CMasher)
+
+Scientific colormaps for making accessible, informative and cmashing plots