Hi ,thanks for the video. i have some questions please , can you tell me which part in the brain those coordinates x,y,z 3,20,36 AND x,y,z 5,-85,-5 , im really wondering about that. thank you
Hi there, These look like human brain coordinates, and unfortunately I don't have experience with those nor do I have a human brain atlas. For a direct answer, you may want to contact someone who does MRI research.
Hi again - I will post what I responded to you with in my email, so that others can view if they have the same question. I will also start a new question on ResearchGate, since I did not find quite the right one after some searching. "Hello Pranali, This is a tricky question to answer - I haven't heard enough talk about a consistent formula among colleagues that did the surgeries. I think it is because the rat skull doesn't elongate evenly across the whole front-to-back span. That said, I'll try to recall what I had done when I did these surgeries, now 7+ years ago. The Paxinos & Watson atlases are modeled after rats that are around 300 grams. For regions anterior to or near bregma, I *think* we added +0.5 mm to the AP coordinate for every 100 grams above the starting 270 gram weight. But if your coordinates are more posterior, perhaps closer to the interaural line, I cannot be sure how much to suggest adding, if any. I decided to look on ResearchGate in case this question was asked & answered there. I only found it for mice (www.researchgate.net/post/Do-I-need-to-correct-for-body-weight-on-AP-coordinate-in-mouse-brain-surgery), but I gleaned a few insights: 1. In this case, we're using weight as a correlate for age - particularly for male rodents. Researchers should be aware if their rodent models have increased fat or muscle gain (either from genes or from experimental diet) that skews that weight upwards from what it should be for a given age. 2. The thread mentions how the brain stops growing in size by adulthood. This is commonly established in many animals. But, I want to add that the skull can still grow a bit in some cases, and this is what ultimately adds error to targeting the brain coordinates. Since I've never worked with mice, I am unsure how well the mouse info tracks with rat situations. I think we should be cautious in assuming it still applies. I also found this thread: www.researchgate.net/post/What-are-the-stereotaxic-coordinates-for-the-lateral-ventricle-in-the-Sprague-Dawley-rats/2 The most helpful comment on page 2 was this: "... the brain/cranium growth is enough to change the coordinates of LV (and other areas). The atlas was designed from rats weighing 270 +/- 20 g, although can be utilized for rats between 250 and 350 g with minimal variation (less than 0.1 mm). Thus, you must utilize rats in this weigh range, or [otherwise] validate the LV coordinates when using mature animals." Another comment recommended using the Waxholm Space atlas of Papp et al. 2014, which they linked via here: scalablebrainatlas.incf.org/ . I don't have time to compare the two atlases, so you may have to investigate on your own. You can continue browsing through the "Questions" portion of ResearchGate to see if another post more directly addresses your question. I scrolled pretty far, and there are still many more questions that came up in the search I used (stereotaxic surgery rat weight), but the vast majority were not quite relevant enough. There are likely more things buried deeper in that search."
I have updates based on answers I received. See the thread again: www.researchgate.net/post/How_do_you_adjust_AP_coordinates_by_body_weight_for_stereotaxic_rat_brain_surgeries Contrary to what I was taught (warned about), this age-related drift in coordinates may not be an issue after all.
Thank you for the video. Can you please help me with the brain region for the following coordinates of rat brain from the bregma 4mm lateral, 2mm anterior and 4mm deep
At a glance, it looks to be the primary somatosensory cortex, "oral dysgranular zone". It's a more internal layer of that cortex, close to the external capsule.
@@paylbajaj I think that's covered to some degree in this video, at 21:40 and beyond. If this video is insufficient, let me know what other information you would need. Is it that the acronyms in the diagram are hard to follow and may not give the full name?
So useful for my exam!!THANK YOU
Glad this was helpful!
Hi ,thanks for the video. i have some questions please , can you tell me which part in the brain those coordinates x,y,z 3,20,36 AND x,y,z 5,-85,-5 , im really wondering about that. thank you
Hi there,
These look like human brain coordinates, and unfortunately I don't have experience with those nor do I have a human brain atlas. For a direct answer, you may want to contact someone who does MRI research.
Hii, useful video sir . I just want to know more about the formula used for calculation of co ordinates according to weight.
Hi again - I will post what I responded to you with in my email, so that others can view if they have the same question. I will also start a new question on ResearchGate, since I did not find quite the right one after some searching.
"Hello Pranali,
This is a tricky question to answer - I haven't heard enough talk about a consistent formula among colleagues that did the surgeries. I think it is because the rat skull doesn't elongate evenly across the whole front-to-back span. That said, I'll try to recall what I had done when I did these surgeries, now 7+ years ago.
The Paxinos & Watson atlases are modeled after rats that are around 300 grams. For regions anterior to or near bregma, I *think* we added +0.5 mm to the AP coordinate for every 100 grams above the starting 270 gram weight. But if your coordinates are more posterior, perhaps closer to the interaural line, I cannot be sure how much to suggest adding, if any.
I decided to look on ResearchGate in case this question was asked & answered there. I only found it for mice (www.researchgate.net/post/Do-I-need-to-correct-for-body-weight-on-AP-coordinate-in-mouse-brain-surgery), but I gleaned a few insights:
1. In this case, we're using weight as a correlate for age - particularly for male rodents. Researchers should be aware if their rodent models have increased fat or muscle gain (either from genes or from experimental diet) that skews that weight upwards from what it should be for a given age.
2. The thread mentions how the brain stops growing in size by adulthood. This is commonly established in many animals. But, I want to add that the skull can still grow a bit in some cases, and this is what ultimately adds error to targeting the brain coordinates.
Since I've never worked with mice, I am unsure how well the mouse info tracks with rat situations. I think we should be cautious in assuming it still applies.
I also found this thread: www.researchgate.net/post/What-are-the-stereotaxic-coordinates-for-the-lateral-ventricle-in-the-Sprague-Dawley-rats/2
The most helpful comment on page 2 was this:
"... the brain/cranium growth is enough to change the coordinates of LV (and other areas). The atlas was designed from rats weighing 270 +/- 20 g, although can be utilized for rats between 250 and 350 g with minimal variation (less than 0.1 mm). Thus, you must utilize rats in this weigh range, or [otherwise] validate the LV coordinates when using mature animals."
Another comment recommended using the Waxholm Space atlas of Papp et al. 2014, which they linked via here: scalablebrainatlas.incf.org/ . I don't have time to compare the two atlases, so you may have to investigate on your own.
You can continue browsing through the "Questions" portion of ResearchGate to see if another post more directly addresses your question. I scrolled pretty far, and there are still many more questions that came up in the search I used (stereotaxic surgery rat weight), but the vast majority were not quite relevant enough. There are likely more things buried deeper in that search."
OK, started a question thread on RG: www.researchgate.net/post/How_do_you_adjust_AP_coordinates_by_body_weight_for_stereotaxic_rat_brain_surgeries
I have updates based on answers I received. See the thread again: www.researchgate.net/post/How_do_you_adjust_AP_coordinates_by_body_weight_for_stereotaxic_rat_brain_surgeries
Contrary to what I was taught (warned about), this age-related drift in coordinates may not be an issue after all.
Thank you for the video. Can you please help me with the brain region for the following coordinates of rat brain from the bregma 4mm lateral, 2mm anterior and 4mm deep
At a glance, it looks to be the primary somatosensory cortex, "oral dysgranular zone". It's a more internal layer of that cortex, close to the external capsule.
Thank you. Can you please make a video on how to identify brain region from the coordinates. That would be highly appreciated..
@@paylbajaj I think that's covered to some degree in this video, at 21:40 and beyond. If this video is insufficient, let me know what other information you would need. Is it that the acronyms in the diagram are hard to follow and may not give the full name?