Creating a Western Blot Figure in ImageJ
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- เผยแพร่เมื่อ 16 ก.พ. 2022
- This demonstrates how to create a figure to display western blot results. Same tools can be used for DNA gel images, thin layer chromatography, Southern blots, silver stain gels and many more.
To learn more you may see user guide
github.com/grishkam/QuickFigu...
For anyone new to QuickFigures, the install instructions and overview are linked below
• Installing QuickFigures
• QuickFigures: 10 Minut...
Thank you so much! Your video was immensely helpful!!!
bro is a genius
In addition, please: are there restrictions on the file types that can be used?
How can I add the Protein ladder
thank you for this demonstration!
however, when i add another image, no cropping windows open, hence if i crop it manually it is of a different size,
Any recommendation?
Thank you!
Unless your image is very small, you should see a crop window. There is an option to Re-Crop all images that can also be used to make crop areas the same size. When you right click on an image panel, you can find the option in the popup menu "Figure
The cropping window is popping once i attached more than one image,
Thank you so much for your help!
How can we align the labels below the image? When I create a new blot figures, the labels automatically get aligned at the top, and I have found no easy way to move them to the bottom and keep automatic alignment. The labels seem to align based on the bottom part, so with angled labels this only works when they are on the top (they will be inside the picture if aligned on the bottom)
Easiest way is to open the "position" dialog for the labels. When a label is selected, there should be an icon below it containing red/blue rectangles. Click that icon. The dialog will appear. In the dialog you can click on the blue rectangle and drag it. Drag it around the area below the red rectangle. The text will change as you drag. When the text says "Upper Corner To Center", the labels should be aligned the way you asked for. You may change the offsets to tweak the positions.
Many thanks. However, why am I not getting the same results as demonstrated here? I moved other cropped TIF images and they are not compatible. I had to convert to PNG files and even at that although it accepted them, but it did not create opportunity for me to individually edit each of the files or "ask me what regions I wanted."
There should be no problem accepting tiff files. In order to figure our exactly why you are having an issue, it would help if you share an example image in either the ImageJ forum or on github. I will take a look at the images as soon as I am able.
Hello I Can not add multiple figure which you describe from 2:27. When I wanted too another sample figure it says This type of file can not be used with this menu option. Do you have any suggestion how should I fix it.
I will work on fixing this issue. What file type were you using? How many channels? Do the same files work when you add them one at a time?
@@quickfigures8341 Yes I had the same file. I am using .tif file. Do I need to install any plug in to open the multiple gel images
Please tell me how I can add the protein ladder
Right click on an image panel, go to the figure submenu and then to the 'add labels' submenu. There is an option to "Add band marks...". After adding the marks, you can edit the locations and labels to match your protein ladder.
Why is it when I click the western blot image tool after putting in the image, I do not get to crop my image and change the angle? Only able to select the region and not the same as 1:10
If either an image is very small or a region of interest is already draw, QuickFigures may skip the crop dialog. If you update QuickFigures now and go to "Edit
When I try to add a second image to my figure (both tiff.files), it says that: "this kind of file cannot be used with this menu option quick figures". When I converted one of the images to png, it only pasted it into my figure, and did not actually allow me to select what bands I want to use from that specific image
Thanks for letting me know. You can add an additional image to a figure either 1) by drag/drop of a file OR 2) using the popup menu that appears when you right click on an existing figure's image panels. If one method gives you that message, you should still be able to use the other method. I will investigate a more permanent fix for the issue.
@@quickfigures8341 Thanks for the reaction, the main thing that gave me trouble is when I try to add a new image using "add" in the bar above. Using the right click method works fine
@@samhillmann9814 The menu options in the add menu of the menu bar can be used to add a new figure to the worksheet or add an independent image panel to the worksheet. None of them are designed to add a new image to an existing figure.
This would be an amazing thing if it wouldn't make my Fiji crash any time I try to do anything 😅
That is disappointing. QuickFigures should not crash. I would like to fix the problem. However, I would need more information. Is there a particular sort of error message you see? What exact circumstances trigger a crash? Perhaps it is specific to your image files?
@@quickfigures8341 I fixed it, it just took stupidly long to save the file
Second question: I can not export to Power Point because it says I need Apache POI 4.1.2. I installed this about 5 times now and it still acts like I haven't. What can I do? I spend a days work on this and I would appreciate some sort of achievement