ThermoCyte: an inexpensive open-source temperature control system for in vitro live cell imaging
Data files
Nov 13, 2023 version files 1.38 MB
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(3a)_-_Temperature_Logs_BV2_microglia_-_Fig._3_A.xlsx
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(3b)_-_Temperature_Logs_BV2_microglia_-_Fig._3_B.xlsx
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(3c)_-_Temperature_Logs_BV2_microglia_-_Fig._3_E.xlsx
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(3d)_-_Temperature_Values_-_IPSC-derived_microglia_-_Fig._9_C.xlsx
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(4a)_Circularity_Values_Room_Temp_-_Fig._5_E.csv
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(4b)_Circularity_Values_Physiological_Temp_-_Fig._5_E.csv
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(5a)_Replicate_1_-_Room_Temp_All_cells_Raw_-_Fig._4-5.csv
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(5b)_Replicate_2_-_Room_Temp_All_cells_Raw_-_Fig._4-5.csv
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(5c)_Replicate_3_-_Room_Temp_All_cells_Raw_-_Fig._4-5.csv
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(5d)_Replicate_1_-_Physiological_Temp_All_cells_Raw_-_Fig._4-5.csv
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(5e)_Replicate_2_-_Physiological_Temp_All_cells_Raw_-_Fig._4-5.csv
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(5f)_Replicate_3_-_Physiological_Temp_All_cells_Raw_-_Fig._4-5.csv
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(5g)_ATP_Stimulation_-_Room_Temp_-_Fig._6.csv
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(5h)_ATP_Stimulation_-_Physiological_Temp_-_Fig._6.csv
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README.md
Abstract
Live-cell imaging is a common technique in microscopy to investigate dynamic cellular behaviour and permits the accurate and relevant analysis of a wide range of cellular and tissue parameters, such as motility, cell division, wound healing responses, and calcium (Ca2+) signalling in cell lines, primary cell cultures, and ex vivo preparations. Furthermore, this can take place under many experimental conditions, making live-cell imaging indispensable for biological research. Systems which maintain cells at physiological conditions outside of a CO2 incubator are often bulky, expensive, and use proprietary components. Here we present an inexpensive, open-source temperature control system for in vitro live cell imaging. Our system ‘ThermoCyte’, which is constructed from standard electronic components, enables precise tuning, control, and logging of a temperature ‘set point’ for imaging cells at physiological temperature. We achieved stable thermal dynamics, with reliable temperature cycling and a standard deviation of 0.42°C over 1 hour. Furthermore, the device is modular in nature, and is adaptable to the researcher's specific needs. This represents simple, inexpensive, and reliable tool for laboratories to carry out custom live-cell imaging protocols, on a standard lab bench, at physiological temperature.
README
ThermoCyte: an inexpensive open-source temperature control system for in vitro live cell imaging
All raw data used in the paper has been uploaded to the Dryad and Zenodo repositories. The data is organised based on order of figures (see below).
In brief, data uploaded includes our 3D-printed stage-top, all Arduino and Python code, all logged raw ThermoCyte temperature values, all BV2 cell circularity values, and all raw BV2 cell pixel intensity traces.
Repository file structure detailed below:
(1) 3D-printed stage-top (Fig. 1, B) was designed using Autodesk TinkerCad, and is made available as an STL file. Open the file using TinkerCad or Prusa Slicer, or a 3D-printing slicing software of your choice that supports STL files (most).
(2) ThermoCyte code (Fig. 1, C) was written in the Arduino IDE. All code is included unedited as .ino files. Open this using Arduino IDE.
(3, a-d) Temperature values (degrees Celcius) from ThermoCyte (Fig. 3, Fig. 9, C) were collected by logging raw temperature readings at 1Hz (1 reading per second) detected by Arduino thermocouples using 'putty', a free SSH and Telnet client. Logs at are included as comma-separated values files (.csv), containing temperature values. Column 'A' in a-c refers to dish temperature, and column 'B' refers to waterblock temperature. In d, column 'B' refers to dish temperature. Integers in column 'A' in a-d are seconds, for Excel graphing purposes only, and can be discarded if necessary. Open these files with Microsoft Excel or Python.
(4, a-b) Circularity values (no units) (Fig. 5, E) were calculated using FIJI (ImageJ) 'shape descriptors' function. Circularity values are included as comma-separated values files (.csv). Open these with Microsoft Excel or Python.
(5, a-h) Pixel intensity traces (arbitrary units) (Fig. 6, Fig. 8) were extracted from raw images. Photobleaching was corrected using napari bleach correct in Napari image viewer, specifically using the 'histogram matching' function (python 3). Motion artefact was corrected using moco plugin in FIJI. Cells were segmented as objects using cellpose 2.0 (Python 3). Mean grey intensity values for each cell were extracted using FIJI 'multi measure' function, and mean grey values for each cell (over time) are included as comma-separated values files (.csv). Open these in Microsfot Excel or Python.
(6) Calcium Peak analysis (Fig. 7 A-D, Fig 8 C, D) was generated from raw pixel intensity data, provided in (5 a-h) above. This was carried out using custom Python code, supplied here as .py files. Open this using python 3; we recommend the 'Anaconda' distribution of Python.
(7) Statistical analysis of calcium peak data (Fig. 7 A-D, Fig 8 C, D) was carried out using custom python code, supplied here as .py files. Open this using python 3; we recommend the 'Anaconda' distribution of Python.
Sharing/Access information
Data may be accessed from Dryad and Zenodo.
O'Carroll, Ross et al. (2023), ThermoCyte: an inexpensive open-source temperature control system for in vitro live cell imaging, Dryad, Dataset, https://doi.org/10.5061/dryad.2280gb5zd
Novel unpublished data was generated in the Dooely Lab, University College Dublin, Dublin, Ireland.
Code/Software
Three scripts are included in the repository:
1 - ThermoCyte code. This Arduino code ('sketch') should be uploaded onto an Arduino Uno rev 3.0, with the Arduino pinout illustrated in Fig. 1, C. Alternatively, you can adapt the code to your own Arduino pinout. The 'LiquidCrystal I2C' library by Frank de Brabander will be required if you are using an I2C LCD. This code is responsible for the main PID (proportional, integral, derivateive) algorithm that ThermoCyte uses to maintain waterblock temperature. It was adapted from code from https://electronoobs.com/eng_arduino_tut24.php.
2 - Calcium Imaging analysis code. This Python code is responsible for processing raw pixel intensity data (5, a-h) from FIJI (imageJ) and performing basic analysis described in the manuscript.
3 - Calcium Imaging analysis and statistics code. This Python code is responsible for processing raw pixel intensity data ((5, a-h)) from FIJI (imageJ), performing basic analysis described in the manuscript, as well as statistical analysis of XY scatter plots (Fig. 7, A and Fig. 8, C).
The Anaconda distribution includes most packages needed for our calcium imaging analysis code to run. The package list for our environment is detailed below.
####### Conda environment package list - Python 3.9.16 ########
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sniffio 1.2.0 py39haa95532_1
snowballstemmer 2.2.0 pyhd3eb1b0_0
sortedcontainers 2.4.0 pyhd3eb1b0_0
soupsieve 2.3.2.post1 py39haa95532_0
sphinx 5.0.2 py39haa95532_0
sphinxcontrib-applehelp 1.0.2 pyhd3eb1b0_0
sphinxcontrib-devhelp 1.0.2 pyhd3eb1b0_0
sphinxcontrib-htmlhelp 2.0.0 pyhd3eb1b0_0
sphinxcontrib-jsmath 1.0.1 pyhd3eb1b0_0
sphinxcontrib-qthelp 1.0.3 pyhd3eb1b0_0
sphinxcontrib-serializinghtml 1.1.5 pyhd3eb1b0_0
spyder 5.4.2 py39haa95532_0
spyder-kernels 2.4.2 py39haa95532_0
sqlalchemy 1.4.39 py39h2bbff1b_0
sqlite 3.41.1 h2bbff1b_0
stack_data 0.2.0 pyhd3eb1b0_0
statsmodels 0.13.5 py39h080aedc_1
sympy 1.11.1 py39haa95532_0
tabulate 0.8.10 py39haa95532_0
tbb 2021.7.0 h59b6b97_0
tbb4py 2021.7.0 py39h59b6b97_0
tblib 1.7.0 pyhd3eb1b0_0
tenacity 8.0.1 py39haa95532_1
terminado 0.17.1 py39haa95532_0
text-unidecode 1.3 pyhd3eb1b0_0
textdistance 4.2.1 pyhd3eb1b0_0
threadpoolctl 2.2.0 pyh0d69192_0
three-merge 0.1.1 pyhd3eb1b0_0
tifffile 2021.7.2 pyhd3eb1b0_2
tinycss2 1.2.1 py39haa95532_0
tk 8.6.12 h2bbff1b_0
tldextract 3.2.0 pyhd3eb1b0_0
tokenizers 0.11.4 py39he5181cf_1
toml 0.10.2 pyhd3eb1b0_0
tomli 2.0.1 py39haa95532_0
tomlkit 0.11.1 py39haa95532_0
toolz 0.12.0 py39haa95532_0
tornado 6.2 py39h2bbff1b_0
tqdm 4.65.0 py39hd4e2768_0
traitlets 5.7.1 py39haa95532_0
transformers 4.24.0 py39haa95532_0
twisted 22.2.0 py39h2bbff1b_1
twisted-iocpsupport 1.0.2 py39h2bbff1b_0
typing-extensions 4.4.0 py39haa95532_0
typing_extensions 4.4.0 py39haa95532_0
tzdata 2022g h04d1e81_0
ujson 5.4.0 py39hd77b12b_0
unidecode 1.2.0 pyhd3eb1b0_0
urllib3 1.26.14 py39haa95532_0
vc 14.2 h21ff451_1
vs2015_runtime 14.27.29016 h5e58377_2
w3lib 1.21.0 pyhd3eb1b0_0
watchdog 2.1.6 py39haa95532_0
wcwidth 0.2.5 pyhd3eb1b0_0
webencodings 0.5.1 py39haa95532_1
websocket-client 0.58.0 py39haa95532_4
werkzeug 2.2.3 py39haa95532_0
whatthepatch 1.0.2 py39haa95532_0
wheel 0.38.4 py39haa95532_0
widgetsnbextension 4.0.5 py39haa95532_0
win_inet_pton 1.1.0 py39haa95532_0
wincertstore 0.2 py39haa95532_2
winpty 0.4.3 4
wrapt 1.14.1 py39h2bbff1b_0
xarray 2022.11.0 py39haa95532_0
xlwings 0.29.1 py39haa95532_0
xz 5.2.10 h8cc25b3_1
yaml 0.2.5 he774522_0
yapf 0.31.0 pyhd3eb1b0_0
zeromq 4.3.4 hd77b12b_0
zfp 0.5.5 hd77b12b_6
zict 2.1.0 py39haa95532_0
zipp 3.11.0 py39haa95532_0
zlib 1.2.13 h8cc25b3_0
zope 1.0 py39haa95532_1
zope.interface 5.4.0 py39h2bbff1b_0
zstandard 0.19.0 py39h2bbff1b_0
zstd 1.5.2 h19a0ad4_0
Methods
- 3D-printed stage-top (Fig. 1, B) was designed using Autodesk TinkerCad, and is made available as STL files.
- ThermoCyte code (Fig. 1, C) was written in the Arduino IDE. All code is included unedited as .ino files.
- Temperature values from ThermoCyte (Fig. 3, Fig. 9, C) were collected by logging raw temperature readings detected by Arduino thermocouples using 'putty', a free SSH and Telnet client. Logs are made available as comma-separated values file (.csv).
- Circularity values (Fig. 5, E) were calculated using ImageJ 'shape descriptors' function. Circularity values are included as a comma-separated values (.csv)
- Pixel intensity traces relating to calcium transients (Fig. 6, Fig. 8) were extracted from raw images. Photobleaching was corrected using napari bleach correct in Napari image viewer, specifically the 'histogram matching' function (python 3). Motion artefact was corrected using moco plugin in FIJI. Cells were segmented as objects using cellpose 2.0 (Python 3). Mean grey intensity values for each cell were extracted using FIJI, and these values for each cell (over time) are provided unedited as a comma-separated values (.csv).
- Calcium Peak analysis (Fig. 7 A-D, Fig 8 C, D) was generated from raw pixel intensity data, provided in (5) above. This was carried out using custom Python code, supplied here as .py files (python 3).
-
Statistical analysis of calcium peak data (Fig. 7 A-D, Fig 8 C, D) was carried out using custom python code, supplied here as .py files (python 3).
Usage notes
- 3D-printed files - Autodesk Tinkercad, Prusa Slicer
- ThermoCyte code - Arduino IDE
- Temperature values - Microsoft Excel
- Circularity Values - Microsoft Excel
- Pixel Intensity Traces - Microsoft Excel, python 3, Important Python packages: Spyder IDE, NumPy, SciPy, Statsmodels, Matplotlib
- Calcium Peak analysis - Microsoft Excel, python 3, Important Python packages: Spyder IDE, NumPy, SciPy, Statsmodels, Matplotlib
- Statistical analysis of calcium peak data - Microsoft Excel, python 3, Major Python packages: Spyder IDE, NumPy, SciPy, Statsmodels, Matplotlib