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CF Strock
Приєднався 8 чер 2013
Biologist with a background in plant physiology, plant nutrition, high throughput phenotyping, data management, and two- and three-dimensional image analysis. Sharing information on these and other topics for undergraduate - graduate students, as well as all others interested in plant biology.
Automated Pipeline for Color Analysis in ImageJ (Fiji)
In this video, I share a macro (available here: doi.org/10.5281/zenodo.5595203) that automates the extraction of summary statistics from channels of three colorspaces (RGB, Lab, and HSB). This macro functions to 1) open an image from a directory folder, 2) threshold the image to segment out the object of interest from the background then "clear" the background so it is completely black, 3) separate the image into the component channels for each color space, 4) extract summary statistics for each channel in each colorspace, 5) export these summary statistics to a .csv file.
I also provide an optional R script (available here: doi.org/10.5281/zenodo.5595203) to automate the reformatting of the .csv file with the summary statistics from the imageJ so each channel is transposed into distinct columns. The final .csv file produced by running this code should have each image as a row, with each summary statistic (mean, mode, min, max, etc.) for each channel in each colorspace presented in a separate column for that image (row).
Step-by-step directions, color analysis macro, and R script available for download here: doi.org/10.5281/zenodo.5595203
ImageJ/Fiji available for download here: imagej.net/software/fiji/
Rstudio available for download here: www.rstudio.com/products/rstudio/
I also provide an optional R script (available here: doi.org/10.5281/zenodo.5595203) to automate the reformatting of the .csv file with the summary statistics from the imageJ so each channel is transposed into distinct columns. The final .csv file produced by running this code should have each image as a row, with each summary statistic (mean, mode, min, max, etc.) for each channel in each colorspace presented in a separate column for that image (row).
Step-by-step directions, color analysis macro, and R script available for download here: doi.org/10.5281/zenodo.5595203
ImageJ/Fiji available for download here: imagej.net/software/fiji/
Rstudio available for download here: www.rstudio.com/products/rstudio/
Переглядів: 7 480
Відео
How to Batch Crop Your Images in ImageJ / Fiji
Переглядів 17 тис.3 роки тому
In this video, I share two options for quick and efficient cropping of large image sets in ImageJ/Fiji. Two options provided are: 1) A protocol to batch crop a set of images as an "image sequence". This approach works best on sets of images that are captured at the same scale and where the region of interest (ROI) is in the same location in every image. 2) A protocol that uses a macro (availabl...
Conducting Hydroponic Studies
Переглядів 8093 роки тому
Here we provide an overview of some considerations for hydroponic studies, including a brief explanation of some of methods used in our work. For more information, visit: plantscience.psu.edu/research/labs/roots
The Center for Root and Rhizosphere Biology at Penn State University
Переглядів 5483 роки тому
Here we provide an overview of ongoing research in the Center for Root and Rhizosphere Biology (CRRB) in the Huck Institute of Life Sciences at Penn State University. Special thanks to Cole Cullen, Creative Director at WPSU who directed and developed this video for the CRRB. For more information on the research of CRRB members, visit: Dr. Ruairidh Sawers, Assistant Professor of Plant Response t...
Conducting Drought Studies in the Greenhouse (Glasshouse)
Переглядів 8023 роки тому
Here we provide an overview of how we conduct studies focused on drought in a greenhouse (glasshouse) setting, including a brief explanation of some of methods used in our work. For more information, visit: plantscience.psu.edu/research/labs/roots
Phosphorus Deficiency Symptoms in Plants
Переглядів 13 тис.3 роки тому
In this video we provide an overview of phosphorus (P) deficiency symptoms in common bean (Phaseolus vulgaris). #NutrientsInANutshell For more information, visit: plantscience.psu.edu/research/labs/roots
Magnesium (Mg) Deficiency Symptoms in Plants
Переглядів 8 тис.3 роки тому
In this video we provide an overview of sulfur (S) deficiency symptoms in common bean (Phaseolus vulgaris). #NutrientsInANutshell For more information, visit: plantscience.psu.edu/research/labs/roots
Sulfur Deficiency Symptoms in Plants
Переглядів 7 тис.4 роки тому
In this video we provide an overview of sulfur (S) deficiency symptoms in common bean (Phaseolus vulgaris). #NutrientsInANutshell For more information, visit: plantscience.psu.edu/research/labs/roots
Nitrogen Deficiency Symptoms in Plants
Переглядів 10 тис.4 роки тому
In this video we provide an overview of nitrogen (N) deficiency symptoms in common bean (Phaseolus vulgaris). #nutrientsinanutshell For more information, visit: plantscience.psu.edu/research/labs/roots
Measuring the Metabolic Costs of the Root System
Переглядів 5464 роки тому
In this video we provide an overview of a protocol for measuring root respiration using the Licor 6400. For more information, visit: plantscience.psu.edu/research/labs/roots
Plant Nutrient Deficiency Symptoms (Nitrogen, Phosphorus, Potassium)
Переглядів 19 тис.4 роки тому
In this video we provide an overview of plant macronutrient deficiency symptoms in maize. For more information, visit: plantscience.psu.edu/research/labs/roots
Measuring Plant Water Potential
Переглядів 8 тис.4 роки тому
In this video we provide an overview of how to measure plant water potential. For more information, visit: plantscience.psu.edu/research/labs/roots
The Maize Root System (Anatomy Sampling)
Переглядів 3,5 тис.4 роки тому
In this video we provide an overview of our methodology for collecting samples from the maize root crown for anatomical analysis. For more information visit: plantscience.psu.edu/research/labs/roots
Measuring Leaf Stomata (Leaf peel/ stomatal peel)
Переглядів 4,9 тис.4 роки тому
Here we provide a methodology for visualizing stomata with light microscopy. For more information visit: plantscience.psu.edu/research/labs/roots
Measuring Leaf Relative Water Content
Переглядів 8 тис.4 роки тому
In this video we provide an overview of the classic methodology for determining leaf relative water content. For more information, visit: plantscience.psu.edu/research/labs/roots
Studying Drought Stress in the Field at Penn State University
Переглядів 1,9 тис.4 роки тому
Studying Drought Stress in the Field at Penn State University
Common bean (Phaseolus vulgaris) root segment with damage from Fusarium
Переглядів 914 роки тому
Common bean (Phaseolus vulgaris) root segment with damage from Fusarium
Common bean (Phaseolus vulgaris) root segment with damage from Fusarium
Переглядів 1094 роки тому
Common bean (Phaseolus vulgaris) root segment with damage from Fusarium
Barley root colonized with cereal cyst nematode
Переглядів 1574 роки тому
Barley root colonized with cereal cyst nematode
Barley (Hordeum vulgare) root segment colonized with cereal cyst nematode
Переглядів 2974 роки тому
Barley (Hordeum vulgare) root segment colonized with cereal cyst nematode
Western corn rootworm colonization and damage in a maize (Zea mays) root segment
Переглядів 734 роки тому
Western corn rootworm colonization and damage in a maize (Zea mays) root segment
Maize (Zea mays) root colonized with western corn rootworm
Переглядів 1694 роки тому
Maize (Zea mays) root colonized with western corn rootworm
Arbuscular mycorrhiza in maize root (3D)
Переглядів 6844 роки тому
Arbuscular mycorrhiza in maize root (3D)
Maize root colonized with arbuscular mycorrhizal fungi
Переглядів 1,4 тис.4 роки тому
Maize root colonized with arbuscular mycorrhizal fungi
Novel application of lasers in plant science research at Penn State University
Переглядів 9724 роки тому
Novel application of lasers in plant science research at Penn State University
what about in case of leaf vegtables
can you make video about difference between iron and solfor deficiencies?
can you make video about difference between iron and solfor deficiencies?
Thank you for this tutorial. Very helpful!
is there any way to follow you on Instagram or anywhere else? so we can connect you and learn things from you thanks
Good Explaination !😀
Ora krungu lik
Em what about the solute potential
does this device takes into account the solute potential
Guys geniune thanks and admiration for this work. Please keep dping it it is phenomenally useful. It is a shame that you have that loud low pitched humming in the back. Easy editing fix and if you get a mic (veey cheap) your awesome info will be crystal clear.
How can a plant that fixes nitrogen become nitrogen deficient?
Hi, i am New in imagej and Hacer a question if could you answer please? İ am trying on one image that selecting multiple rois and want to for each roi apply crop, duplicate , add gray,Binary.......and skeletonise. Making it step bu step so bored. İ tried to make a macro but i failured. Can you help me please how can i handle. Thanks
This is awesome! Thank you for the tips.
How could someone crop ROIs that are indifferent locations but make them the same size and also rotate/reorient them individually
did you figure it out? xx
@@kiarad2242 Yes. Essentially it involves creating a rotated rectangle, moving and rotating over portion to keep, and then duplicating. The straighten command also works in place of duplicate, but I have a feeling it could technically cause distortion
Good job Chris, keep it up:)
Thank you so much! Really worked like a charm.
Great video. I do similar work in a crop phys lab at NCSU. Do you have any publications which list the materials and equipment used in this setup?
excellent video! Cheers from Italy
Thank you vewry much for your explanation. I have a question here, I read "Rapid Estimates of Relative Water Content" and at the end i was pretty confused how to measure the RWC.
Is there any way to use the second method where you manually select your region of interest but also ensure that the cropped images have the same dimensions. In this case they are all different sizes
did you figure it out? I'm struggling with the same thing right now
@@kiarad2242 yes gotcha! What I do now is I select what I want to crop, then I go to edit -> selection -> specify. Then I specify the dimensions I want, then you can drag and move the box to the exact spot. Then press ctrl + x to crop I believe. I haven't got this to work as a macro, but I just do this individually to each image that I want to crop, but still be uniformly sized.
O my God, I wish to watch your video before I started my working on my research. Am also working on drought at greenhouse however I need more information from you dude, before I start collecting my data.
Very nice script, just one question. Is it possible to do this measurements in the different particles within the same picture? let me explain, I'm trying to measure the emission of seedlings in petri dishes and will be very useful if I can do it by plant
Thank you!
This has helped my data analysis so much <3
Hello, Sir! That's amazing. May I ask if you could also upload video about measuring water use efficiency of plants ? Thank youu!!
Thank you very much
thanks for this informative video. I'm a little confused as to why/how saturation and brightness values are above 100 in your HSB data set. are brightness and saturation not measured on a scale from 1-100? if not, what is the scale, so I can convert this number in to a percent? thanks again for your help!
I keep getting this error: Error in value_vars(value.var, names(data)) : value.var values [c("Area1", "Mean1", "StdDev1", "Mode1", "Min1", "Max1")] are not found in 'data'. Would you possibly be able to help with this? :) Thanks
Thank you sir, very helpful for my GFP-brightfield-merged image series!
Hi! I ran into some problems with the program mistaking the object for the background and I don't know if you would be able to help me. When I run the program at first it looks fine since it shows the background black but when looking at the measured images at the end it shows the other way around, with the object as black. I don't know if the final image is wrong or just the entire process. I tried both automatic and customized thresholding. Thanks
Hi Jing- Definitely sounds like a thresholding issue/incorrect thresholding settings for your images. The summary stats from all the channels will reflect the pixels that are not blacked-out in your final images that are saved back to your working directory. I think the solution lies in finding the correct thresholding values for your specific image set.
@@CFStrock Hi. I don't know why but I couldn't find the correct thresholding values so the object doesn't go black. In the end, since I'm working with beakers which have an easy shape, I decided to crop them by hand. Thank you for answering though!
Thanks for the helpful video!!!!!!!!!!!!!!! Helps a lot!
lol xd
dude im an agriculture student, and your videos are so cool!
This is honestly incredible work! is there any way to obtain the raw data? E.g. if I didn't want the mean A value for CIELAB but instead all the A values of all the pixels? Thank you
Thank you so much! Just what I needed!
hi, please how do I download the whole color macro_all component?
available here: doi.org/10.5281/zenodo.5595203
This is some cool shit!
I'm going to name my first child CF Strock
👌👌🙏
What is effects of excessive nitrogen in plants.
No solutions?
Brilliant man! Thank you for your service.
Hi, the video is very helpful, thank. But my images is passing too fast. How can I slow down it?
Do not play the image sequence. DO not push the triangle button
Hi! Thanks for this illustrative video and the protocol! Everything works fine
Thank you
thank u love u
excuse me sir. can you make video tutorial of image batch masking with fiji ? thankyouu
hi, can you talk about humic acid and fulvic acid where they come from and benefit
Do you have issues with algae with the white containers? Great videos, I would love to see more hydroponics videos.
Really helpful videos, thanks for sharing! Seeing the toxicity would be great too!
Amazing work