COBA-NIH · github-actions · Apr 11, 2026
diff --git a/_build/gettext/01_Sample_preparation.pot b/_build/gettext/01_Sample_preparation.pot
@@ -8,7 +8,7 @@ msgid ""
 msgstr ""
 "Project-Id-Version: Python \n"
 "Report-Msgid-Bugs-To: \n"
-"POT-Creation-Date: 2024-03-29 09:37-0400\n"
+"POT-Creation-Date: 2026-04-11 14:17+0000\n"
 "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
 "Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
 "Language-Team: LANGUAGE <LL@li.org>\n"
@@ -123,7 +123,7 @@ msgid "Some whole organisms are thin and transparent enough to image. Some anima
 msgstr ""
 
 #: ../../01_Sample_preparation/Considerations.md:69
-msgid "Imaging whole organisms or embyros provides the most possible intact biological context when studying a particular process or structure."
+msgid "Imaging whole organisms or embryos provides the most possible intact biological context when studying a particular process or structure."
 msgstr ""
 
 #: ../../01_Sample_preparation/Considerations.md:73

diff --git a/_build/gettext/02_Sample_acquisition.pot b/_build/gettext/02_Sample_acquisition.pot
@@ -8,7 +8,7 @@ msgid ""
 msgstr ""
 "Project-Id-Version: Python \n"
 "Report-Msgid-Bugs-To: \n"
-"POT-Creation-Date: 2025-05-23 21:07+0000\n"
+"POT-Creation-Date: 2026-04-11 14:17+0000\n"
 "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
 "Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
 "Language-Team: LANGUAGE <LL@li.org>\n"
@@ -47,7 +47,7 @@ msgid "**Confocal** - microscopes that remove out-of-focus light in the light pa
 msgstr ""
 
 #: ../../02_Sample_acquisition/Introduction.md:12
-msgid "**Multiphoton** microscopes utilize multiple pulses of longer-wavelength (lower energy) light to penetrate deep into tissue, since tissues are less likely to scatter these wavelengths; once there, multiple low-engergy photons hitting the fluorphore at the same time will use their combined energy to activate a fluorophore that each photon alone would be too weak to do. Because the benefit of these systems is in their deeper penetration, they are often used for performing live-animal imaging."
+msgid "**Multiphoton** microscopes utilize multiple pulses of longer-wavelength (lower energy) light to penetrate deep into tissue, since tissues are less likely to scatter these wavelengths; once there, multiple low-energy photons hitting the fluorophore at the same time will use their combined energy to activate a fluorophore that each photon alone would be too weak to do. Because the benefit of these systems is in their deeper penetration, they are often used for performing live-animal imaging."
 msgstr ""
 
 #: ../../02_Sample_acquisition/Introduction.md:13
@@ -107,7 +107,7 @@ msgid "Microscope objectives have a number of features that must be considered w
 msgstr ""
 
 #: ../../02_Sample_acquisition/Practical_considerations.md:9
-msgid "Magnification and resolution: the higher the numerical aperture (NA) of the lens, the finer the resolution one can obtain in one's sample. The NA is calculated as {math}`NA=RI * sin(θ)`, relating both to the {term}`refractive index` of the sample, glass, and {term}`immersion media` as well as the range of angles of emitted light that can be collected into the lens. Unless special techniques are used, the typical limit of resultion is calculated as {math}`d = λ / 2NA`, meaning the resolution is set both by the NA of the lens but also by the wavelength of light used for imaging."
+msgid "Magnification and resolution: the higher the numerical aperture (NA) of the lens, the finer the resolution one can obtain in one's sample. The NA is calculated as {math}`NA=RI * sin(θ)`, relating both to the {term}`refractive index` of the sample, glass, and {term}`immersion media` as well as the range of angles of emitted light that can be collected into the lens. Unless special techniques are used, the typical limit of resolution is calculated as {math}`d = λ / 2NA`, meaning the resolution is set both by the NA of the lens but also by the wavelength of light used for imaging."
 msgstr ""
 
 #: ../../02_Sample_acquisition/Practical_considerations.md:18
@@ -131,23 +131,23 @@ msgid "Filter sets"
 msgstr ""
 
 #: ../../02_Sample_acquisition/Practical_considerations.md:26
-msgid "It is important to make sure that the microscope that you want to image on has the correct filter sets for the fluorphores you wish to use. See the [section on bleedthrough](content/bleedthrough) for more information."
+msgid "It is important to make sure that the microscope that you want to image on has the correct filter sets for the fluorophores you wish to use. See the [section on bleedthrough](content/bleedthrough) for more information."
 msgstr ""
 
 #: ../../02_Sample_acquisition/Practical_considerations.md:28
 msgid "Z sampling"
 msgstr ""
 
 #: ../../02_Sample_acquisition/Practical_considerations.md:30
-msgid "If you wish to capture multiple z sections, the spacing of these setions is important if you wish to be able to perform an accurate 3D reconstruction. SVI has a [fuller mathematical explanation of this](https://svi.nl/NyquistRate),as well as an easy-to-use [online calculator](https://svi.nl/NyquistCalculator) that you can use to calculate the optimal z section spacing for your imaging conditions."
+msgid "If you wish to capture multiple z sections, the spacing of these sections is important if you wish to be able to perform an accurate 3D reconstruction. SVI has a [fuller mathematical explanation of this](https://svi.nl/NyquistRate),as well as an easy-to-use [online calculator](https://svi.nl/NyquistCalculator) that you can use to calculate the optimal z section spacing for your imaging conditions."
 msgstr ""
 
 #: ../../02_Sample_acquisition/Practical_considerations.md:32
 msgid "Acquisition power/speed"
 msgstr ""
 
 #: ../../02_Sample_acquisition/Practical_considerations.md:34
-msgid "The amount of signal captured from any fluorophore will be related not just to the intrinsic brightness of the fluorophore, but also the amount of excitation light it is exposed to (due to duration, power, or both) as well as amount of time and signal multiplication that happens at the detector (typically a camera or a photomultiplier tube (PMT)). An optimal experiment is typically one that minimizes the amount of light hitting the sample (to reduce photobleaching and/or phototoxicity) while acheiving adequate fluorescent signal and in minimal time on the equipment. How exactly to balance these competing factors will depend on the exact biology being studied and the researcher's constraints."
+msgid "The amount of signal captured from any fluorophore will be related not just to the intrinsic brightness of the fluorophore, but also the amount of excitation light it is exposed to (due to duration, power, or both) as well as amount of time and signal multiplication that happens at the detector (typically a camera or a photomultiplier tube (PMT)). An optimal experiment is typically one that minimizes the amount of light hitting the sample (to reduce photobleaching and/or phototoxicity) while achieving adequate fluorescent signal and in minimal time on the equipment. How exactly to balance these competing factors will depend on the exact biology being studied and the researcher's constraints."
 msgstr ""
 
 #: ../../02_Sample_acquisition/Resources.md:1

diff --git a/_build/gettext/03_Image_analysis.pot b/_build/gettext/03_Image_analysis.pot
@@ -8,7 +8,7 @@ msgid ""
 msgstr ""
 "Project-Id-Version: Python \n"
 "Report-Msgid-Bugs-To: \n"
-"POT-Creation-Date: 2025-05-23 21:07+0000\n"
+"POT-Creation-Date: 2026-04-11 14:17+0000\n"
 "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
 "Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
 "Language-Team: LANGUAGE <LL@li.org>\n"
@@ -127,7 +127,7 @@ msgid "Colocalization is when two or more different labels (e.g., eGFP and mCher
 msgstr ""
 
 #: ../../03_Image_analysis/Colocalization.md:8
-msgid "It is also important to recognize that co-ocurrence does not _necessarily_ imply interaction."
+msgid "It is also important to recognize that co-occurrence does not _necessarily_ imply interaction."
 msgstr ""
 
 #: ../../03_Image_analysis/Colocalization.md:11
@@ -538,7 +538,7 @@ msgid "Microscopy images are inherently quantitative, which makes them a very po
 msgstr ""
 
 #: ../../03_Image_analysis/Introduction.md:26
-msgid "The specifics of your workflow depend on your biological question. Below we present a few common types of analysis for fluorescence microscopy experiments. For each, we’ll explain key ideas to understand before you begin, common pitfalls, and links to a few key resources to learn more. We encourage you to think about your analysis strategy even before beginning sample preparation. While not always possible, speaking with an image analysis expert{cite}`Cimini2024-uh` in your local core facility or asking a question on the [image.sc](https://image.sc) forum _before you begin_ can save you a ton of time and headache when it comes to designing an image analysis strategy. Some general concepts are also covered in a recent short review{cite}`."
+msgid "The specifics of your workflow depend on your biological question. Below we present a few common types of analysis for fluorescence microscopy experiments. For each, we’ll explain key ideas to understand before you begin, common pitfalls, and links to a few key resources to learn more. We encourage you to think about your analysis strategy even before beginning sample preparation. While not always possible, speaking with an image analysis expert{cite}`Cimini2024-uh` in your local core facility or asking a question on the [image.sc](https://image.sc) forum _before you begin_ can save you a ton of time and headache when it comes to designing an image analysis strategy. Some general concepts are also covered in a recent short review{cite}`Cimini2024-sz`."
 msgstr ""
 
 #: ../../03_Image_analysis/Introduction.md:28

diff --git a/_build/gettext/04_Data_presentation.pot b/_build/gettext/04_Data_presentation.pot
@@ -8,7 +8,7 @@ msgid ""
 msgstr ""
 "Project-Id-Version: Python \n"
 "Report-Msgid-Bugs-To: \n"
-"POT-Creation-Date: 2025-05-23 21:07+0000\n"
+"POT-Creation-Date: 2026-04-11 14:17+0000\n"
 "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
 "Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
 "Language-Team: LANGUAGE <LL@li.org>\n"
@@ -38,7 +38,7 @@ msgid "What is it?"
 msgstr ""
 
 #: ../../04_Data_presentation/Presentation_images.md:5
-msgid "Microscopy images are often shown in scientific papers to illustrate a particular conclusion. While qualitative conclusions are not a subsitute for quantitative comparisons (see next section), images can certainly guide our reasoning and our conclusions. Following a few consistent best practices ensures that these conclusions are correct and robust."
+msgid "Microscopy images are often shown in scientific papers to illustrate a particular conclusion. While qualitative conclusions are not a substitute for quantitative comparisons (see next section), images can certainly guide our reasoning and our conclusions. Following a few consistent best practices ensures that these conclusions are correct and robust."
 msgstr ""
 
 #: ../../04_Data_presentation/Presentation_images.md:14
@@ -165,7 +165,7 @@ msgid "Explain the image"
 msgstr ""
 
 #: ../../04_Data_presentation/Presentation_images.md:95
-msgid "To rapidly orient audiences, a minimal explanatory text should be presented along with images. This includes the figure legend and the methods section in scientific papers or the title of figures in posters and slides. Consider using a controlled vocabulary to reduce ambiguity and increase machine-readability of the descriptions of specimens, tissues, cell lines, and proteins etc. A useful tool is the [RRID (Reseach Resource Identifying Data)index](https://scicrunch.org/resources) , which provides indices for commonly used biological reagents and resources, e.g., plasmids, cell lines and antibodies ."
+msgid "To rapidly orient audiences, a minimal explanatory text should be presented along with images. This includes the figure legend and the methods section in scientific papers or the title of figures in posters and slides. Consider using a controlled vocabulary to reduce ambiguity and increase machine-readability of the descriptions of specimens, tissues, cell lines, and proteins etc. A useful tool is the [RRID (Research Resource Identifying Data)index](https://scicrunch.org/resources) , which provides indices for commonly used biological reagents and resources, e.g., plasmids, cell lines and antibodies ."
 msgstr ""
 
 #: ../../04_Data_presentation/Presentation_images.md:101
@@ -261,7 +261,7 @@ msgid "Statistics"
 msgstr ""
 
 #: ../../04_Data_presentation/Statistics.md:5
-msgid "Quantitative data is often summarized and analysed with statistical methods and visualized with plots/graphs/diagrams. Statistical methods reveal quantitative trends, patterns, and outliers in data, while plots and graphs help to convey them to audiences. Carrying out a suitable statistical analysis and choosing a suitable chart type for your data, identifying their potential pitfalls, and faithfully realising the analysis or generating the chart with suitable software are essential to back up experimental conclusions with data and reach communication goals."
+msgid "Quantitative data is often summarized and analyzed with statistical methods and visualized with plots/graphs/diagrams. Statistical methods reveal quantitative trends, patterns, and outliers in data, while plots and graphs help to convey them to audiences. Carrying out a suitable statistical analysis and choosing a suitable chart type for your data, identifying their potential pitfalls, and faithfully realizing the analysis or generating the chart with suitable software are essential to back up experimental conclusions with data and reach communication goals."
 msgstr ""
 
 #: ../../04_Data_presentation/Statistics.md:7
@@ -329,15 +329,15 @@ msgid "Normality testing"
 msgstr ""
 
 #: ../../04_Data_presentation/Statistics.md:58
-msgid "Normality testing is about assessing whether data follow a Gaussian (or nomal) distribution. Because the Gaussian distribution is frequently found in nature and has important mathematical properties, normality is a core assumption in many widely-used statistical tests. When this assumption is violated, their conclusions may not hold or be flawed. Normality testing is therefore an important step of the data analysis pipeline prior to any sort of statistical testing."
+msgid "Normality testing is about assessing whether data follow a Gaussian (or normal) distribution. Because the Gaussian distribution is frequently found in nature and has important mathematical properties, normality is a core assumption in many widely-used statistical tests. When this assumption is violated, their conclusions may not hold or be flawed. Normality testing is therefore an important step of the data analysis pipeline prior to any sort of statistical testing."
 msgstr ""
 
 #: ../../04_Data_presentation/Statistics.md:61
 msgid "Normality of a data distribution can be qualitatively assessed through plotting, for instance relying on a histogram. For a more quantitative readout, statistical methods such as the Kolmogorov-Smirnov (KS) and Shapiro-Wilk tests (among many others) report how much the observed data distribution deviates from a Gaussian. These tests usually return and a p-value linked to the hypothesis that the data are sampled from a Gaussian distribution. A high p-value indicates that the data are not inconsistent with a normal distribution, but is not sufficient to prove that they indeed follow a Gaussian. A p-values smaller than a pre-defined significance threshold (usually 0.05) indicates that the data are not sampled from a normal distribution."
 msgstr ""
 
 #: ../../04_Data_presentation/Statistics.md:65
-msgid "Although lots of the “standard” statistical methods have been designed with a normnality assumption, alternative approaches exist for non-normally-ditributed data. Many biological processes result in multimodal “states” (for instance differentiation) that are inherently not Gaussian. Normality testing should therefore not be mistaken for a quality assessment of the data: it merely informs on the types of tools that are appropriate to use when analyzing them."
+msgid "Although lots of the “standard” statistical methods have been designed with a normality assumption, alternative approaches exist for non-normally-distributed data. Many biological processes result in multimodal “states” (for instance differentiation) that are inherently not Gaussian. Normality testing should therefore not be mistaken for a quality assessment of the data: it merely informs on the types of tools that are appropriate to use when analyzing them."
 msgstr ""
 
 #: ../../04_Data_presentation/Statistics.md:68

diff --git a/_build/gettext/Glossary.pot b/_build/gettext/Glossary.pot
@@ -8,7 +8,7 @@ msgid ""
 msgstr ""
 "Project-Id-Version: Python \n"
 "Report-Msgid-Bugs-To: \n"
-"POT-Creation-Date: 2024-03-29 09:37-0400\n"
+"POT-Creation-Date: 2026-04-11 14:17+0000\n"
 "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
 "Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
 "Language-Team: LANGUAGE <LL@li.org>\n"
@@ -129,7 +129,7 @@ msgid "Refractive index"
 msgstr ""
 
 #: ../../Glossary.md:44
-msgid "It's a measure of how light travels through a specific medium. It is an important value when calculating the numerical aperture of an objective, Ideally, a mismatch in refractive index between the sample (mounting medium), the coverslip and immersion media should be minimized in order to enhance the image quality. [See an interactive demo of refactive index at MicroscopyU](https://www.microscopyu.com/microscopy-basics/refractive-index-index-of-refraction)"
+msgid "It's a measure of how light travels through a specific medium. It is an important value when calculating the numerical aperture of an objective, Ideally, a mismatch in refractive index between the sample (mounting medium), the coverslip and immersion media should be minimized in order to enhance the image quality. [See an interactive demo of refractive index at MicroscopyU](https://www.microscopyu.com/microscopy-basics/refractive-index-index-of-refraction)"
 msgstr ""
 
 #: ../../Glossary.md:42
@@ -153,7 +153,7 @@ msgid "Semantic segmentation, where all parts of an image are part of a class, c
 msgstr ""
 
 #: ../../Glossary.md:52
-msgid "Instance segmentation, the segmentation is object based, not just detecting were the cells are but diving each cell as a separate object."
+msgid "Instance segmentation, the segmentation is object based, not just detecting where the cells are but diving each cell as a separate object."
 msgstr ""
 
 #: ../../Glossary.md:53

diff --git a/_build/gettext/QuantitativeBioimaging.pot b/_build/gettext/QuantitativeBioimaging.pot
@@ -8,7 +8,7 @@ msgid ""
 msgstr ""
 "Project-Id-Version: Python \n"
 "Report-Msgid-Bugs-To: \n"
-"POT-Creation-Date: 2024-03-29 09:37-0400\n"
+"POT-Creation-Date: 2026-04-11 14:17+0000\n"
 "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
 "Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
 "Language-Team: LANGUAGE <LL@li.org>\n"
@@ -45,7 +45,7 @@ msgid "Have I selected analysis metric(s) that truly answer my biological questi
 msgstr ""
 
 #: ../../QuantitativeBioimaging.md:12
-msgid "Have I chosen appropriate statistical comparisons and data presentation approaches so that the distribution of my metric(s) can be fairly compared across samples, answering my biolgical question?"
+msgid "Have I chosen appropriate statistical comparisons and data presentation approaches so that the distribution of my metric(s) can be fairly compared across samples, answering my biological question?"
 msgstr ""
 
 #: ../../QuantitativeBioimaging.md:14