abstr work

comments.md

@@ -1,9 +1,17 @@
 * Q: Should the title be the same as the `methods-paper` version published on bioRxiv?
   - i.e. If there is/was a singular conclusive message of wide interest that could be pointed to, then perhaps that could be the title, but this one is still likely good, especially with the Results and figure data being the same.
-* Q: Would the isofl data help with this manuscript? Or maybe the idea of integrating any new material is a too much now 
+  - our work shows non-random overlap in the mesoscale domain mosaic between recordings, suggesting cortical organization itinerant, persistent functional units/motifs 
+* Q: Would the isofl data help with this manuscript? Or maybe the idea of integrating any new material is too much now 
 * Q: Should a measure of information rate per recording be reported?
     - i.e. the data flow amounts in and out of optimized vs non-optimized imaging sessions
 
+<!-- * Q: What is the dynamic range of our cortical calcium signal before and after filtration? (e.g. raw data vs rICA data) -->
+<!-- * Q: How many bits of the cameras ADC are needed to encode our calcium signal variance? What about for calcium signal variance+hemodynamic variance+vascular artifact variance all together on the same monochromatic channel? -->
+
+* possible things to highlight: 
+    - domains or components per recording, spatial characteristics of the domains, diam
+    * jaccard overlap of the regions or domains between sequential recordings or different animals
+
 ---
 
 ## Abstract
@@ -75,6 +83,7 @@
 
 * [ ] 6. def What is baseline
     - the controls are non/less-time variant tissue fluoresence vs high dynamic range neuronal calcium signals 
+    - expl, cite resting state activity, fmri study timeframes? (which also do not usually have a quantified baseline timeframe)
 
 * [ ] 7. local vs global signals
     - n components, size, px counts, common modes
@@ -85,9 +94,31 @@
 
 * [ ] 10. Then leads to: Where the calcium flux comes from, multi spots, small comp in opp hemisphere from the larger singular src blobs, axon traj or max prob of tissue src origination
 
-
+* [ ] highlight the age more? This work is on a cohort of of mice having a postnatal age of 21 days. 
 
 
 ## Results
 
 * [x] Check when Fig. S6 is referred to in text
+* [ ] Check the um/px value for the lateral spatial resolution
+* [ ] Check colormap dots overlay in figureS7
+* [ ] Check writing of figure7 legend
+* [ ] Check Allen Brain atlas map31 in figure7 legend
+* [ ] rw "to test the meaning of these maps" 
+* [ ] Highlight the substantial Jaccard index for region overlap (and domain overlap) between recordings and  
+
+* [ ] Check phrase 'detected regions' as in 'We additionally quantified whether detected regions...'
+
+* [ ] Fix Figure S6 "Nueral"
+
+
+## Methods
+
+* [ ] rw 'components that are unsorted and often flipped'
+* [ ] rw 'mean time series is pre-subtracted from the array before SVD'SVD used before defined in next paragraph. The mean signal effect is removed with the pre-whitening/sphereing step of SVD 
+
+* [ ] rw, clarify Map creation domain size as in: 'This map was then further processed to get rid of domains smaller than 1/10th the mean domain. Any domain smaller than this size'
+* [ ] rw, clarify 'Olfactory bulbs were included in map generation, but domains were highly variable, and were excluded'
+* [ ] check sentence 'same number of domains or regions as the original map, n, and shares the same cortical mask as the original map. To create this map, n points were distributed randomly across the cortical mask. To turn these points into regions, the voronoi diagram was created using the scipy spatial package35'
+* [ ] check sentence 'When comparing maps generated from different animals, the optimal alignment was calculated by shifting the second map up to 100 pixels in any direction. The optimal direction was determined by maximizing the Jaccard overlap.'
+