Hi! Thanks a lot for your videos! They have help me a lot! I have a question regarding the Batch. I´m doing split channels (Blue, Green, Red), then selecting the green and counting the spots as you indicated. Until here, everything Ok. However, when I run the Macro in Batch, the program does not recognize the the names of the others green files (only recognizes the original one, those with I set up the Macro). Any idea of how to solve it? Thanks!.
Hello, Apologies for the delayed response. I am having a busy week. I will experiment with my data to work out a plausible solution. For now, can you split your macro into three, this will take less than 30 sec per image; 1. To process the image before the merging part, 2. To merge the image (this will require you to open one image at a time to use this steps). 3. To finish the last part of the analysis you are conducting. Cheers
@@AliceritaE Hi! I solved it! After I split the image, a "said to the macro" "close" the first open window (that in my case was the blue channel). After that, . the program automatically take the next "open window" to count the particles, that in my case was the green one, those that I was interesting in counting. Thank you again a lot! Let's keep in contact. Cheers!
Alicerita!! THANK YOU SO MUCH!! I was stucked with 2800 images that I needed to resize and process, and your video was so helpful!! Greetings fron Chile!
Hello Alicerita. Thank you for your informative video. I am measuring colocalization of antibodies with/without treatment. I am using the JaCOP plugin to get pearson's correlation and Mander's coefficient. It works fine with 1 image. My problem is when I recorded my Macro and apply them to all my images. Apparently, it is only analysing just 1 type of image in a folder of 32 images. I think what is happening is that the Macro recorded the name of that particular image, and therefore it only processes that image in the selected folder. Do you know how to deal with this problem? Note that my image is .lsm format. It has 3 channels, green, red, and blue. After I split channels, I always remove blue (DAPI) because it is not relevant for my analysis. Sorry for the lengthy comment!
Hello, Thanks for your message. If the macro is recognising just a single image. I'll recommend to open all the images in imageJ, then apply the macro to each image to get the quantification. I have had similar problem in tje past, i just apply the macro to each image to get the quantification data. In less than 10 min, you should finish the analysis. Cheers!
Hi Alicerita, thank you so much your videos have really helped me out! I had no issues following your first tutorial on how to record a macro for one image. However, I am having issues implementing my macro for a batch. When I try to do this for a number of images I create from X,Y coordinates, I use the same macro script which is: run("Duplicate...", " "); run("Convex Hull"); setForegroundColor(255, 255, 255); run("Fill", "slice"); setOption("BlackBackground", false); run("Convert to Mask"); selectWindow("1_96741891097.txt"); close(); But I get the following error: "Selection required in line 2 run in ("Convex Hull" ;" I'm not sure why this is, and I was hoping you may have some insight. Thank you.
Hi Louise, Thank you for your kind feedback. The reason the macro is not working for the batch is because it contains a sample name "1.9..." You have to edit the macro to not include the sample name. Let me know If that helps. Cheers
@@AliceritaE No problem, thanks for such a speedy response! I have tried removing the sample name (I mistakenly included it when I pasted my macro) and I still get the same error message when I run the following macro for my batch: run("Duplicate...", " "); run("Convex Hull"); setForegroundColor(255, 255, 255); run("Fill", "slice"); setOption("BlackBackground", false); run("Convert to Mask"); Thank you.
In that case, the last resolve i can recommend is to open all the files, and manually apply the macro to each image, then save. (I have personally done this when the macros fails to comply)
@@AliceritaE Re your previous message, yes I will follow that advice for now as that seems to be the best course of action. And thank you so much! I'm new to this and the documentation is overwhelming, but I will do my best to research some answers too :)
I’m using ImageJ count the number if particles on images. I’ve written a macro that seems to work reasonably well to do this. However, when I run it, the “summary” window repopulates every one to two images…therefore I get A LOT of windows to manually rename, save, and copy data from to an excel file. Is there an “easy” way to accomplish getting all the image counts to display in one “summary” window? Or even to just automatically move all the lines of data into an Excel sheet for saving?
It's stressful when imageJ does that. However, you can go to set measurement and tick the display sample name among the several parameter. That way, when inageJ repopulate the summary page with several measurements, you can have a single excel file for your data. You can then later filter the excel file by sample name. This way, you don't have to manually copy to an excel sheet.
thank you! I'm wondering how I can use a macro on a batch if it includes a file name. My macro includes duplicating an image and using it to redirect brightness values after thresholding. How can I make this work on every file in a folder if they all have different file names?
Hi, thanks for sharing! It’s very helpful. But I have a problem that I need to split two colour channels and save both of them, but after batch processing, it only save one channel of the two channels. So do you have any idea how to deal with this? Also could you please tell me where is that “said to macro” window from the top commenter, as I’m struggling to find it. Many thanks!
// ask user to select a folder dir = getDirectory("Select A folder"); // get the list of files (& folders) in it fileList = getFileList(dir); // prepare a folder to output the images output_dir = dir + File.separator + "output" + File.separator ; File.makeDirectory(output_dir); //activate batch mode setBatchMode(true); // LOOP to process the list of files for (i = 0; i < lengthOf(fileList); i++) { // define the "path" // by concatenation of dir and the i element of the array fileList current_imagePath = dir+fileList[i]; // check that the currentFile is not a directory if (!File.isDirectory(current_imagePath)){ // open the image and split open(current_imagePath); // get some info about the image getDimensions(width, height, channels, slices, frames); // if it's a multi channel image if (channels > 1) run("Split Channels"); // now we save all the generated images as tif in the output_dir ch_nbr = nImages ; for ( c = 1 ; c
Hi Alicerita, 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
thank you so much Alicerita. I have a problem with my analysis using macros batch processing. Could I ask you from your Facebook? or do you have any other social medias where you are more active there? Please answer 😁
Ok, let me explain it here, if possible. I am beginner for using macro. I have to measure the distance among 5 dots in each photo. There are 300 photos. I tried to make the dots by using "multi points or point" command then Ctrl+ m to measure them. After that I got "X and Y" value. However, it will be difficult to run it manually for each photo. Do you know how to make the script for Macros for doing this? It would be great if you want to answer my question.
Hi! Thanks a lot for your videos! They have help me a lot! I have a question regarding the Batch. I´m doing split channels (Blue, Green, Red), then selecting the green and counting the spots as you indicated. Until here, everything Ok. However, when I run the Macro in Batch, the program does not recognize the the names of the others green files (only recognizes the original one, those with I set up the Macro). Any idea of how to solve it? Thanks!.
Hello, Apologies for the delayed response. I am having a busy week. I will experiment with my data to work out a plausible solution.
For now, can you split your macro into three, this will take less than 30 sec per image;
1. To process the image before the merging part,
2. To merge the image (this will require you to open one image at a time to use this steps).
3. To finish the last part of the analysis you are conducting.
Cheers
@@AliceritaE Don't worry. I appreciate a lot your help! I will follow your recommendation. If you reach to solve it, please, let me know. Thanks!
You're welcome, I have added this to my to do list. I will update you accordingly.
@@AliceritaE Hi! I solved it! After I split the image, a "said to the macro" "close" the first open window (that in my case was the blue channel). After that, . the program automatically take the next "open window" to count the particles, that in my case was the green one, those that I was interesting in counting. Thank you again a lot! Let's keep in contact. Cheers!
This is great!
Thank you for updating with your findings
Your video taught me more in 9 minutes than I learned in hours of reading tutorials. Thank you so so much!
thank you for your kind feedback.
Alicerita!! THANK YOU SO MUCH!! I was stucked with 2800 images that I needed to resize and process, and your video was so helpful!! Greetings fron Chile!
Thank you @Dominique Ducros I am glad you found the video helpful
You are literally a life saver :) Please continue to make more ImageJ videos
Thank you @Maria camila rodriguez
Thank you so much! This is going to save me a TON of time!
You're welcome, Kelly!
your tutorial is very easy to understand. thank you😊
You're welcome!
Can't wait to try this! Thank you!
You're welcome, please let me know how you get along.
Another wonderful video Alice
Thank you 😊
Great tutorial! Thank you!
Hi Melanie, I'm glad you found the tutorial useful. Thanks for watching
Very helpful, thank you!
Hi Luiza, I'm glad you found my tutorial helpful. Have a wonderful weekend. Cheers!
Very helpful. Thanks a lot!!!!!!!!!!
You're welcome 😊
Hello Alicerita. Thank you for your informative video. I am measuring colocalization of antibodies with/without treatment. I am using the JaCOP plugin to get pearson's correlation and Mander's coefficient. It works fine with 1 image. My problem is when I recorded my Macro and apply them to all my images. Apparently, it is only analysing just 1 type of image in a folder of 32 images. I think what is happening is that the Macro recorded the name of that particular image, and therefore it only processes that image in the selected folder. Do you know how to deal with this problem? Note that my image is .lsm format. It has 3 channels, green, red, and blue. After I split channels, I always remove blue (DAPI) because it is not relevant for my analysis. Sorry for the lengthy comment!
Hello,
Thanks for your message. If the macro is recognising just a single image. I'll recommend to open all the images in imageJ, then apply the macro to each image to get the quantification.
I have had similar problem in tje past, i just apply the macro to each image to get the quantification data.
In less than 10 min, you should finish the analysis.
Cheers!
Hi Alicerita, thank you so much your videos have really helped me out!
I had no issues following your first tutorial on how to record a macro for one image.
However, I am having issues implementing my macro for a batch.
When I try to do this for a number of images I create from X,Y coordinates, I use the same macro script which is:
run("Duplicate...", " ");
run("Convex Hull");
setForegroundColor(255, 255, 255);
run("Fill", "slice");
setOption("BlackBackground", false);
run("Convert to Mask");
selectWindow("1_96741891097.txt");
close();
But I get the following error:
"Selection required in line 2
run in ("Convex Hull" ;"
I'm not sure why this is, and I was hoping you may have some insight.
Thank you.
Hi Louise,
Thank you for your kind feedback. The reason the macro is not working for the batch is because it contains a sample name "1.9..."
You have to edit the macro to not include the sample name. Let me know If that helps. Cheers
@@AliceritaE No problem, thanks for such a speedy response! I have tried removing the sample name (I mistakenly included it when I pasted my macro) and I still get the same error message when I run the following macro for my batch:
run("Duplicate...", " ");
run("Convex Hull");
setForegroundColor(255, 255, 255);
run("Fill", "slice");
setOption("BlackBackground", false);
run("Convert to Mask");
Thank you.
In that case, the last resolve i can recommend is to open all the files, and manually apply the macro to each image, then save. (I have personally done this when the macros fails to comply)
I will try and test your script when i am with pc. I will like to know how to over come the error message
@@AliceritaE Re your previous message, yes I will follow that advice for now as that seems to be the best course of action. And thank you so much! I'm new to this and the documentation is overwhelming, but I will do my best to research some answers too :)
I’m using ImageJ count the number if particles on images. I’ve written a macro that seems to work reasonably well to do this. However, when I run it, the “summary” window repopulates every one to two images…therefore I get A LOT of windows to manually rename, save, and copy data from to an excel file. Is there an “easy” way to accomplish getting all the image counts to display in one “summary” window? Or even to just automatically move all the lines of data into an Excel sheet for saving?
It's stressful when imageJ does that. However, you can go to set measurement and tick the display sample name among the several parameter. That way, when inageJ repopulate the summary page with several measurements, you can have a single excel file for your data. You can then later filter the excel file by sample name.
This way, you don't have to manually copy to an excel sheet.
thank you! I'm wondering how I can use a macro on a batch if it includes a file name. My macro includes duplicating an image and using it to redirect brightness values after thresholding. How can I make this work on every file in a folder if they all have different file names?
when there are multiple step to go through. I normally just open all the images and manually apply thr macro to each
Informative.
#AVMCreations
Hi, thanks for sharing! It’s very helpful. But I have a problem that I need to split two colour channels and save both of them, but after batch processing, it only save one channel of the two channels. So do you have any idea how to deal with this? Also could you please tell me where is that “said to macro” window from the top commenter, as I’m struggling to find it. Many thanks!
Here is a code I found on ImageJ platform that helped another users with their task
// ask user to select a folder
dir = getDirectory("Select A folder");
// get the list of files (& folders) in it
fileList = getFileList(dir);
// prepare a folder to output the images
output_dir = dir + File.separator + "output" + File.separator ;
File.makeDirectory(output_dir);
//activate batch mode
setBatchMode(true);
// LOOP to process the list of files
for (i = 0; i < lengthOf(fileList); i++) {
// define the "path"
// by concatenation of dir and the i element of the array fileList
current_imagePath = dir+fileList[i];
// check that the currentFile is not a directory
if (!File.isDirectory(current_imagePath)){
// open the image and split
open(current_imagePath);
// get some info about the image
getDimensions(width, height, channels, slices, frames);
// if it's a multi channel image
if (channels > 1) run("Split Channels");
// now we save all the generated images as tif in the output_dir
ch_nbr = nImages ;
for ( c = 1 ; c
@@AliceritaEwow! Thanks! Let me have a try!
Hi Alicerita, 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
Hi, you need to firer get it work on one video before the automating. Check out this other video. th-cam.com/video/V2mO4MC0dho/w-d-xo.html
if your set of images has a different resolution, how can you set a script with an if statement because the distance is not the same in all images?
I will experiment with this. I haven't try the IF command before. I will update you with my findings
thank you so much Alicerita. I have a problem with my analysis using macros batch processing. Could I ask you from your Facebook? or do you have any other social medias where you are more active there? Please answer 😁
Hi Rahayu, I am available here to answer your questions 😊
What's is the problem you encountered
Ok, let me explain it here, if possible. I am beginner for using macro. I have to measure the distance among 5 dots in each photo. There are 300 photos. I tried to make the dots by using "multi points or point" command then Ctrl+ m to measure them. After that I got "X and Y" value. However, it will be difficult to run it manually for each photo. Do you know how to make the script for Macros for doing this? It would be great if you want to answer my question.
Hi, are the photos in .tiff or .jpeg format?
@@AliceritaE all photos in .tiff format