Next generation CANCAN focusing for remote stimulation by nanosecond electric pulses (DANDI:001025)

Claims

From the paper Next generation CANCAN focusing for remote stimulation by nanosecond electric pulses

Reproducing Pakhomov et al. (2023) from dandiset 001025 4

Notebook reproduce_pakhomov_2023.ipynb

Not reproduced4

Not reproducedResults, 3.3, paragraph 2; Figure 7Aquestion to the reader
On the small array with 1Px4, raising the first pulse amplitude from 2.4 to 5.6 kV increases YP fluorescence 15.5 times at the most peripheral point, 16.2 times half-way to the center and 16.8 times in the center.
when the first pulse amplitude was increased from 2.4 to 5.6 kV (and the amplitude of the other pulses in the packet was increased proportionally, see Fig. 2C ), YP fluorescence increased 15.5 times at the most peripheral point; 16.2 times half-way to the center; and 16.8 times in the center ( Fig. 7A ).
Results, 3.3, paragraph 2; Figure 7A
Without background subtraction, as the criterion fixes, the 5.6 over 2.4 kV ratios of dish means under the main reading are 5.99 at the most peripheral ROI, 5.65 half-way and 7.25 at the centre (4 dishes at 2.4 kV, 3 at 5.6 kV). Over all 18 readings they range from 5.11 to 6.35, 5.31 to 6.01 and 5.93 to 7.59, and none is within tolerance. Leaving out any one 2.4 kV dish changes them by at most 0.59, and dropping the end ROIs inside the paper's 5% exclusion zone gives 5.77, 5.84 and 7.25. With the median inside the needle footprints subtracted (150.7 a.u. on average at 2.4 kV, 375.9 at 5.6 kV), a variant the criterion excludes, the main reading gives 13.37, 15.87 and 15.16 (two of three within tolerance), 2 of 18 readings put all three within tolerance, and with the exclusion-zone ROIs also dropped all three are within it (14.88, 17.10 and 15.16). At the pixel size implied by the needle footprints (a variant) the ratios are 5.71, 5.45 and 7.32 without background and 14.17, 14.82 and 15.39 with it. The outcome turns on whether an offset was removed. The criterion says none is, "as in the Methods"; the Methods do not say, and whether the claims file reads the paper correctly here is asked of a reader in questions/001025.yaml.
How the test differed from the paper’s method
- The paper measured the ROIs in MetaMorph with the electrode positions known; the dandiset holds no ROIs or electrode positions, so the electrodes are found by fitting four dark disks to each image and the ROIs are placed from their centre (overlays in the notebook).
- The pixel size is not in the dataset. 0.65 um is used, from the ORCA-Flash4.0 camera and 10x objective the files name, assuming no binning. The dark footprint of each needle has a median radius of 0.650 mm (large array) and 0.718 mm (small array) at this scale, against the 0.75 mm radius of the 1.5 mm needles (Section 2.3). The footprints rule out the round-1 variant at which the large diagonal is 8.4 mm (0.591 um), which puts the needle edge inside the paper's ROI span on both arrays and is dropped, but they do not confirm the camera scale; they imply 0.679 um (small array) and 0.750 um (large array), at which the large diagonal is 10.65 mm, further from the paper's 8.4 mm than the 9.23 mm of the camera scale. The camera scale is kept for the main reading and the footprint scale is run as a variant; it does not change this claim's result.
- At the camera scale the paper's ROI spans (Section 2.4) end 0.12 mm (small array) and 0.22 mm (large array) from the needle edge, inside the paper's exclusion zone of 5% of the diagonal (0.25 and 0.46 mm). The spans are kept as the paper states them; a variant drops the end ROIs inside the zone.
- ROI width across the diagonal is not given (Section 2.4); square ROIs are used, a choice that changes only how many pixels are averaged.
- The packet is not named in the session descriptions ("CanCan protocol ... 12.5% lower"); Packet 2 is assumed, as in Fig. 7 and the dandiset's title.
- The dandiset has 4 dishes at 2.4 kV where Figure 7 states n = 3; all four are used and each leave-one-out is shown.
Not reproducedResults, 3.3, paragraph 2; Figure 7Brests on an assumption
Normalized to the most peripheral ROI, the profiles for different first pulse amplitudes fully overlap, so the spatial distribution of electroporation, and NG-CANCAN targeting, does not depend on amplitude within the studied range.
In contrast, changing nsEP amplitude affected the degree of electroporation but not its spatial distribution ( Fig. 7 ). ... When the YP emission was normalized to the most peripheral ROI, the data for different nsEP amplitudes fully overlapped ( Fig. 7B ).
Results, 3.3, paragraph 2; Figure 7B
Under the main reading 1 of 20 voltage pairs differs at p < 0.05, the normalised centre at 2.4 kV (108.6%) against 4.8 kV (136.9%), p = 0.0037; no half-way pair differs (smallest p = 0.12). The pair stays significant whichever 2.4 kV dish is left out (p = 0.0012 to 0.0116). The readings disagree, 10 of 36 (18 layouts by 2 normalisations) give no significant pair and 26 give one to five. With no effect, the chance of at least one p below 0.05 among the 20 uncorrected tests would be 0.64 if they were independent; they share groups and dishes, and a simulation of this design gives 0.47 with the two positions correlated as in the data (r = 0.64). p = 0.0037 would not pass a Bonferroni threshold for 20 tests (0.0025), which the criterion does not apply. The normalised centre means lie between 108.6% and 136.9% across the five voltages. With the footprint background subtracted (a variant the claims file excludes) the main reading finds no pair (smallest p = 0.18), and 30 of 36 readings find none; whether a background should be removed is asked of a reader (questions/001025.yaml). With the end ROIs inside the exclusion zone dropped, 4 of 20 pairs differ without background and 2 of 20 with it. At the pixel size implied by the needle footprints the same pair differs without background (p = 0.0279) and no pair with it (smallest p = 0.14). Over all ROIs of the folded profile, 23 of 220 tests are below 0.05.
How the test differed from the paper’s method
- Assumed the main reading of the ROI layout (92 ROIs over both diagonals, both diagonals averaged, one ROI centred on the array centre, raw ROI means, normalisation to the mean of the end ROIs). The paper leaves each of these open (Section 2.4; claims file, opening comment); the reasons are given in the notebook (the Fig. 5B legend averages both diagonals for rotated packets, the Methods give one ROI count, the paper reports measured values). The outcome rests on it, as 10 of 36 readings find no difference.
- Electrode detection, pixel size, exclusion zone, ROI width and packet as for fig7a-amplitude-scales-uptake.
- The voltages (2.4, 3.2, 4.0, 4.8 and 5.6 kV) are taken from the dataset, as the criterion says; 2.4 kV has 4 dishes where the paper states n = 3.
Not reproducedResults, 3.3, paragraph 2; Figure 7C and 7Drests on an assumption
The independence of the normalized distribution from amplitude also holds when rotating multiple packets (10Px4) on the larger array.
The findings held true for rotating multiple packets and when using the larger array ( Fig. 7C and D ). Overall, our results show that NG-CANCAN targeting of electroporation does not depend on nsEP amplitude, at least within the studied amplitude range.
Results, 3.3, paragraph 2; Figure 7C and 7D
The dandiset holds two voltages for the large array with 10Px4, 4.8 kV (2 dishes) and 6.4 kV (3 dishes). Under the main reading the normalised centre is 232.6% against 126.0%, p = 0.0494, and the half-way values do not differ (94.8% against 46.8%, p = 0.16). Both 4.8 kV dishes (270.6% and 194.7%) lie above all three 6.4 kV dishes (102.4% to 149.8%). 27 of 36 readings find no difference, and with the footprint background subtracted the main reading gives p = 0.0705 (25 of 36 readings find none), so the outcome rests on the main reading and a two-dish group; with 2 dishes against 3 a non-significant reading could not show the absence either. With the end ROIs inside the exclusion zone dropped the centre differs more clearly (p = 0.0173; 0.0089 with background subtracted). At the pixel size implied by the needle footprints the difference is gone (249.5% against 226.6%, p = 0.57; p = 0.25 with background subtracted), so the outcome also rests on the camera scale. The a.u. values rise from 4.8 to 6.4 kV at all three positions (ratios 3.53 at the periphery, 1.89 half-way, 2.00 at the centre).
How the test differed from the paper’s method
- Only two voltages, one with 2 dishes, where the paper shows Figure 7C and 7D with n = 3 and voltages marked in the figure; the others are not in the dandiset.
- Assumed the main reading of the ROI layout, as for fig7b-targeting-independent-of-amplitude; the outcome rests on it, and on the camera pixel size (the footprint scale, a variant, finds no difference).
- Electrode detection, pixel size, exclusion zone, ROI width and packet as for fig7a-amplitude-scales-uptake.
Not reproducedDiscussion, paragraph 5; Figure 7rests on an assumption
Remote targeting, within the studied limits, depends neither on pulse amplitude nor on array size, so findings from small arrays can be extrapolated to larger inter-electrode distances.
the remote targeting, at least within studied limits, did not depend on either the electric pulse amplitude or array size ( Fig. 7 ). We infer that findings from small electrode arrays can be extrapolated to larger inter-electrode distances.
Discussion, paragraph 5; Figure 7
The criterion requires fig7b-targeting-independent-of-amplitude and fig7cd-holds-for-large-array to be reproduced; neither is, under the main reading. The folded normalised profiles reach, at their first position (the mean of the two grid ROIs beside the centre, each dish normalised to its end ROIs), 109.5% to 140.1% on the small array (1Px4) and 145.0% to 212.3% on the large one (10Px4); the two arrays received different packet numbers, so array size is not isolated.
How the test differed from the paper’s method
- Rests on the main reading assumed for the two claims it depends on, on the camera pixel size (fig7cd), and on the claims file's reading that no background is subtracted.

Not tested in a notebook 10

2 data missing from the dataset, 8 other

Blocked10

BlockedResults, 3.1, paragraph 2; Figure 4· Data missing from the dataset
A single unipolar 600-ns pulse at 15 kV/cm causes by far the strongest YP uptake in individual CHO cells, 126 +/- 14 a.u. at the end of the 10-min recording (n = 25), and sham exposure causes no gain in YP fluorescence.
Sham-exposed cells showed no gain in YP fluorescence during the 10 min of observation. ... A single 600-ns pulse at 15 kV/cm caused by far the strongest YP uptake, reaching 126±14 a.u. (n=25) by the end of recording.
Results, 3.1, paragraph 2; Figure 4
The dandiset holds only monolayer images. The confocal time-lapse images of single cells between two electrodes (Section 2.2) are not in it, nor in any other dandiset that cites the paper (000686, 000875, 001027 and 001028 hold monolayer images of Figures 5, 6, 8 and 9); a search of DANDI for the lab's other dandisets found none that holds them.
BlockedResults, 3.1, paragraph 2; Figure 4 legend· Data missing from the dataset
Bipolar signals that start with the same pulse cause significantly weaker YP uptake than the single unipolar pulse (p < 0.001), reaching 20.8 +/- 2.0 a.u. for the 4-phase signal, 6.9 +/- 1.6 a.u. for the 8-phase signal and 25.4 +/- 2.8 a.u. for the 8-phase signal with 5-us delays; the 8-phase signal gives about 20-fold cancellation.
Bipolar signals started with exactly the same pulse (600 ns, 15 kV/cm) but caused significantly weaker effects (p<0.001). By the end of recording, YP signal reached only 20.8±2.0 a.u. for the 4-phasic signal; 6.9±1.6 a.u. for the 8-phasic signal; and 25.4±2.8 a.u. for the 8-phasic signal with 5-μs delays between phases. The impressive 20-fold bipolar cancellation achieved with the 8-phasic signal
Results, 3.1, paragraph 2; Figure 4 legend
What the paper reports
- each bipolar signal against the single unipolar pulse, end of recording: p < 0.001 (n = 21 to 30 cells per group)
As fig4-unipolar-strongest; the single-cell time-lapse data are not public on DANDI.
BlockedResults, 3.2, paragraph 1; Figure 5A· Other
Packet 2 applied 40 times from e1 enhances electroporation in the center of the array despite the weakening field, while the unipolar train control electroporates more strongly throughout and follows the field distribution; without rotation the region near e1 stays stronger than the center.
The lack of cancellation caused a much stronger electroporation throughout the array, and the distribution of YP uptake expectedly followed the electric field strength distribution in Fig. 3C . In contrast, Packet 2 enhanced electroporation in the center of the array, despite gradual weakening of the electric field with distance from e1. However, the bipolar cancellation only partially offset the electric field weakening, and electroporation near e1 remained stronger than in the center.
Results, 3.2, paragraph 1; Figure 5A
No dish of this dandiset received 40 packets or 40 trains from e1; its 21 images are the 1Px4 and 10Px4 treatments of Figure 7. The Figure 5 images appear to be in dandiset 000686 ("Focusing electroporation to the center of a quadrupole electrode array by interference of unipolar pulses"), which cites the same paper and is a target of its own; the claims file gives this claim as data from this dataset, so it is not tested here.
BlockedResults, 3.2, paragraph 1; Figure 5B and 5C· Other
Rotating the first-energized electrode with Packet 2 (1Px40) smears the effect at the perimeter and emphasizes a remote effect in the center, while the same rotation of the unipolar train (1Tx40) leaves a void of electroporation in the center; the difference is clearest in fluorescence normalized to the most peripheral ROI.
Rotation with Packet 2 “smeared” the electroporation effect at the perimeter and emphasized the remote effect in the center. This remote effect contrasted with a void of electroporation in the center when the pulse train was applied in the same manner instead of the packet.
Results, 3.2, paragraph 1; Figure 5B and 5C
No 1Px40 or 1Tx40 dishes in this dandiset; see fig5a-center-enhanced-without-rotation (dandiset 000686).
BlockedResults, 3.3, paragraph 1; Figure 6A· Other
Increasing the total number of rotated Packet 2 packets from 4 to 20 and 40 strongly increases YP uptake throughout the array, and the central peak is discernible for all three.
Increasing the total number of applied packets from 4 to 20 and 40 profoundly enhanced the electroporative YP dye uptake throughout the electrode array ( Fig. 6A ). The peak of electroporation in the center was clearly discernable for all tested treatments.
Results, 3.3, paragraph 1; Figure 6A
This dandiset has no 5Px4 dishes, and its 1Px4 and 10Px4 dishes are on different arrays (small and large, from the electrode spacing), so no packet-number series on one array. The Figure 6 images appear to be in dandiset 000875 ("Influence of unipolar pulse packet quantity on centering the electroporation effect"), which cites the same paper and is a target of its own.
BlockedResults, 3.3, paragraph 1; Figure 6B· Other
Normalized to the periphery, the central peak is almost twofold for 1Px4 and about the same as the periphery for 5Px4 and 10Px4; the trough between center and electrodes is about twofold lower than the center for all treatments; the central peak becomes narrower with more packets.
Its brightness was almost twofold higher than at the periphery for a single packet was applied 4 times from different directions, or about the same as at the periphery for the rotation of 5 and 10 packets ( Fig. 6B ). Interestingly, the least affected area of the cell monolayer (between the center and the electrodes) showed about 2-fold lower fluorescence intensity than in the center for all the treatments. Also, the central peak appeared narrower (sharper) with increasing the number of packets.
Results, 3.3, paragraph 1; Figure 6B
As fig6a-more-packets-more-uptake (dandiset 000875).
BlockedResults, 3.4, paragraph 2; Figure 8A· Other
Packets 1, 2 and 3 (4 kV, 1Px4) produce the same YP uptake in the center (215 to 235 a.u.), but Packets 1 and 3 cause much more uptake near the electrodes (250 to 350 a.u.) than Packet 2 (about 120 a.u.), p < 0.01.
All packets produced the same YP uptake in the center (215–235 a.u.), but Packets 1 and 3 caused drastically more YP uptake near the electrodes (250–350 a.u. vs ~120 a.u. for packet 1, p<0.01, Fig. 8A ).
Results, 3.4, paragraph 2; Figure 8A
What the paper reports
- Packets 1 and 3 against Packet 2, near the electrodes: two-sided Student's t-test (Methods, 2.4), p < 0.01 (n = 3 to 4 dishes per packet)
All dishes of this dandiset received Packet 2; no Packet 1 or Packet 3 dishes. The Figure 8 images appear to be in dandiset 001027 ("CANCAN focusing of electroporation in a quadrupole array by different pulsing protocols"), which cites the same paper and is a target of its own. The 4.0 kV 1Px4 dishes here may be the Packet 2 group of Figure 8, but the comparison needs the other packets. Set against the paper's Packet 2 values (not deciding the claim), they read 614.9 a.u. at the periphery and 718.8 a.u. in the centre (353.8 and 457.7 with the footprint background subtracted), against about 120 and 215 to 235 a.u., and their normalised centre is 118.8% (137.3% with background subtracted) against 183%.
BlockedResults, 3.4, paragraph 2; Figure 8B· Other
Normalized to the most peripheral ROI, YP emission in the center drops from 183% for Packet 2 to 83% for Packet 3 and 74% for Packet 1, so the packet with the strongest bipolar cancellation targets best.
The superiority of Packet 2 for CANCAN targeting is highlighted by the drop of normalized YP emission in the center from 183% for Packet 2 to 83% and 74% for Packets 3 and 1, respectively ( Fig. 8B ).
Results, 3.4, paragraph 2; Figure 8B
As fig8a-packets-differ-near-electrodes (dandiset 001027).
BlockedResults, 3.5, paragraph 1; Figure 9A and 9B· Other
Raising the large array 1, 2 and 3 mm above the monolayer reduces YP emission near the electrodes 2.4, 6.4 and 9 times but in the center only 1.02, 1.4 and 3.8 times, raising the targeting efficiency (center over periphery) to as much as 600% at 2 mm.
Specifically, YP emission near the electrodes decreased 2.4, 6.4, and 9 times with 1-, 2- and 3-mm gaps (as compared to electrodes being in the same plane with cells); in the center, it decreased just 1.02, 1.4, and 3.8 times, respectively. Such disproportionally faster fading of the effect near electrodes boosted the CANCAN targeting efficiency (measured as a ratio of the effect in the center and at the periphery) to as much as 600% for the 2-mm gap ( Fig. 9B ).
Results, 3.5, paragraph 1; Figure 9A and 9B
No dish of this dandiset was treated with the array above the monolayer. The Figure 9 images appear to be in dandiset 001028 ("CANCAN focusing of electroporation in 3D"), which cites the same paper. The 6.4 kV 10Px4 large-array dishes here match the 0 mm condition, but the gaps are missing. Their profile is printed in the notebook. The centre ROI of the main reading is 126.0% of the end ROIs; the first position of the folded profile (the mean of the two grid ROIs beside the centre), the value used for discussion-independent-of-array-size, is 145.0%. The text gives no a.u. for the 0 mm group to compare them with.
BlockedResults, 3.5, paragraph 1; Figure 9C· Other
With the electrodes above the monolayer, electroporation is restricted almost exclusively to the center of the array.
YP fluorescence images in Fig. 9C show that electroporation is restricted almost exclusively to the remote target (center) when electrodes are placed above the cell monolayer.
Results, 3.5, paragraph 1; Figure 9C
As fig9-gap-boosts-targeting (dandiset 001028).

Findings about the data

What attempts found about the dataset itself, for its owner and the archive.

Data missingThe dandiset holds only the 21 monolayer images of Figure 7. The images of Figures 5, 6, 8 and 9 appear, from their titles and descriptions, to be in four other dandisets that cite the same paper (000686, 000875, 001027 and 001028), which the dandiset does not mention, and the single-cell time-lapse data of Figure 4 are in no dandiset that cites the paper.
Description missingNo pixel size is given (the ImageSeries resolution attribute is 96 or 1, not a pixel size), the array (small or large) is not stated, and the electrode positions, the electrode labels e1 to e4 and the paper's ROI measurements are not included. The array can be inferred from the electrode spacing, and it matches the protocol in every file.
Description missing7 of the 21 files name no detector, objective or channel, and the 5 large-array files hold a second channel labelled DAPI that the paper does not describe.
Metadata errorSubject ids do not identify dishes. sub-15 and sub-25 each hold two dishes imaged on different days under different protocols (2.4 kV 1Px4 and 4.8 kV 10Px4; 5.6 kV and 3.2 kV 1Px4), so the archive counts 19 subjects for 21 dishes, while each dish was used in one experiment (Section 2.1).
Selection not documentedFigure 7 states n = 3 for every voltage. The dandiset has 4 dishes at 2.4 kV, 3 at 3.2, 4.0, 4.8 and 5.6 kV on the small array, and for the large array only 4.8 kV (2 dishes) and 6.4 kV (3 dishes). Which 2.4 kV dish the paper left out, and the other large-array voltages, are not documented.
Methods not availableQuestion for the paper's authors. Was a background (camera offset or the intensity of unlabelled regions) subtracted from the ROI values before the fold changes of Section 3.3 and the normalisations of Figure 7? The images have a dark floor of 33 to 81 a.u. that varies between dishes and sessions. Without subtraction the 5.6 over 2.4 kV ratios here are 5.7 to 7.3, against 15.5 to 16.8 in the paper; with the median of the electrode footprints subtracted they are 13.4 to 15.9.
Methods not availableQuestion for the paper's authors. How were the 92 and 224 ROIs laid out (per diagonal or over both, their width, which diagonals for Figure 7), what is the pixel size of the stitched images, and how is the 8.4 mm diagonal of the large array measured? At the 0.65 um pixel of the named camera and objective the electrode centres of the large array are 9.2 mm apart on the diagonal, and the paper's ROI spans end inside its own 5% exclusion zone; the needle footprints imply a larger pixel still (0.75 um, a 10.65 mm diagonal), at which the comparison of Figure 7D finds no difference. Under the readings of the layout, the voltage comparisons of Figure 7B and 7D find a significant pair in 26 of 36 and 9 of 36 readings, so the outcomes of fig7b and fig7cd rest on the reading assumed.
Description missingThe session descriptions name the CANCAN protocol with 12.5% decrements but not the packet (Packets 1, 2 and 3 all use that decrement); Packet 2 is inferred from the dandiset's title and Figure 7.
OtherThe 4.0 kV 1Px4 dishes, the Packet 2 condition of Figure 8 if Figure 8 used the small array (its legend does not say), read 614.9 a.u. at the periphery and 718.8 a.u. in the centre, against about 120 and 215 to 235 a.u. in Section 3.4, so the paper's a.u. do not appear to be the raw image values, or these are not the Figure 8 dishes. The paper does not say how its a.u. relate to the images.

Questions

Where the author or a verifier believed the claims file misread the paper, they asked, citing the paper, and a reader who had not seen the data answered from the paper alone, amending the claims file where it was wrong. The author then ran the claim as answered. Attempts before protocol pilot-11 also asked here for method details the claims file did not give.

openasked 2026-11-02about fig7a-amplitude-scales-uptake
The criterion says "the paper does not say whether background is subtracted from the a.u. values, and none is, as in the Methods". The Methods for the monolayer experiments (Section 2.4) say nothing either way, and Section 2.2 does correct for background (F - F0) for the single-cell data. Does the paper support "none is subtracted", or should the criterion leave the background open, as a reading (none, or a background such as the camera offset or the unlabelled area removed) the way the opening comment treats the ROI layout? The same question bears on fig7b-targeting-independent-of-amplitude and fig7cd-holds-for-large-array, whose normalised values change with it.
Passage. Section 2.4, "Fluorescence intensity was measured with MetaMorph 7.8.13 (Molecular Devices, Foster City, CA) as a function of the distance from the geometrical center of the electrode array" (no word on background). Section 2.2, "Emission intensity corrected for the background (F-F0) was used for graphs and statistical analyses." Section 3.4 gives Packet 2 at 4 kV, 1Px4 as about 120 a.u. near the electrodes and 215 to 235 a.u. in the centre.
Why it matters. The images carry an offset that varies by session (dark floor 33 to 81 a.u., median inside the needle footprints 140 to 425 a.u.). Without subtraction the 5.6 over 2.4 kV ratios of fig7a are 5.99, 5.65 and 7.25 (none within tolerance in 18 readings); with the footprint median subtracted they are 13.37, 15.87 and 15.16 under the main reading, and 14.88, 17.10 and 15.16 (all within tolerance) when the end ROIs inside the paper's exclusion zone are also dropped. For fig7b the one significant pair under the main reading (p = 0.0037) disappears with the background subtracted (smallest p = 0.18; 30 of 36 readings find no pair). The dataset's 4.0 kV 1Px4 dishes read about 615 a.u. at the periphery and 719 a.u. in the centre, so the paper's a.u. do not look like raw values. The verifier of round 1 reported this as a possible misreading of the paper by the claims file.
No reader has answered it yet.

Notebooks

Every registered entry that uses this dataset. An entry can hold several notebooks, and can use more than one dataset.

Reproduction NG-CANCAN focusing of electroporation and pulse voltage (Pakhomov et al. 2023)

Tests the findings of Pakhomov, Gudvangen, Mangalanathan, Kondratiev, Redondo and Semenov (2023) on dandiset 001025, which holds one stitched YO-PRO-1 image per dish for the experiments of Figure 7, Packet 2 rotated once on the small quadrupole array at 2.4 to 5.6 kV and ten times on the large array at 4.8 and 6.4 kV. The notebook finds the electrodes in each image, places the paper's ROIs along the diagonals and compares fluorescence and its normalised profile across voltages. The single-cell data of Figure 4 and the experiments of Figures 5, 6, 8 and 9 are not in the dandiset. All files

Reproducing Pakhomov et al. (2023) from dandiset 001025
reproduce_pakhomov_2023.ipynbExecuted, with outputs · Source

Verification

Round 1
2026-11-02Agreed with 14 of 14 outcomes. Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook). Reviewed: The handover of the author-answers run (commit 998836cf4), the executed notebook with the conclusions and summary removed, the helper module and the claims file, with the paper under paper/.
Round 2
2026-11-02Agreed with 14 of 14 outcomes. Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook). Reviewed: The full executed notebook of the author-revise-1 run (commit f8df3d1f3), with its conclusions and summary, the helper module, the claims file and the attempt record, with the paper under paper/.

Method differences

How the tests differed from the paper’s method or data, and the claims each applies to.

Electrode detection, pixel size, exclusion zone, ROI width and packet as for fig7a-amplitude-scales-uptake.fig7b-targeting-independent-of-amplitude fig7cd-holds-for-large-array
The paper measured the ROIs in MetaMorph with the electrode positions known; the dandiset holds no ROIs or electrode positions, so the electrodes are found by fitting four dark disks to each image and the ROIs are placed from their centre (overlays in the notebook).fig7a-amplitude-scales-uptake
The pixel size is not in the dataset. 0.65 um is used, from the ORCA-Flash4.0 camera and 10x objective the files name, assuming no binning. The dark footprint of each needle has a median radius of 0.650 mm (large array) and 0.718 mm (small array) at this scale, against the 0.75 mm radius of the 1.5 mm needles (Section 2.3). The footprints rule out the round-1 variant at which the large diagonal is 8.4 mm (0.591 um), which puts the needle edge inside the paper's ROI span on both arrays and is dropped, but they do not confirm the camera scale; they imply 0.679 um (small array) and 0.750 um (large array), at which the large diagonal is 10.65 mm, further from the paper's 8.4 mm than the 9.23 mm of the camera scale. The camera scale is kept for the main reading and the footprint scale is run as a variant; it does not change this claim's result.fig7a-amplitude-scales-uptake
At the camera scale the paper's ROI spans (Section 2.4) end 0.12 mm (small array) and 0.22 mm (large array) from the needle edge, inside the paper's exclusion zone of 5% of the diagonal (0.25 and 0.46 mm). The spans are kept as the paper states them; a variant drops the end ROIs inside the zone.fig7a-amplitude-scales-uptake
ROI width across the diagonal is not given (Section 2.4); square ROIs are used, a choice that changes only how many pixels are averaged.fig7a-amplitude-scales-uptake
The packet is not named in the session descriptions ("CanCan protocol ... 12.5% lower"); Packet 2 is assumed, as in Fig. 7 and the dandiset's title.fig7a-amplitude-scales-uptake
The dandiset has 4 dishes at 2.4 kV where Figure 7 states n = 3; all four are used and each leave-one-out is shown.fig7a-amplitude-scales-uptake
Assumed the main reading of the ROI layout (92 ROIs over both diagonals, both diagonals averaged, one ROI centred on the array centre, raw ROI means, normalisation to the mean of the end ROIs). The paper leaves each of these open (Section 2.4; claims file, opening comment); the reasons are given in the notebook (the Fig. 5B legend averages both diagonals for rotated packets, the Methods give one ROI count, the paper reports measured values). The outcome rests on it, as 10 of 36 readings find no difference.fig7b-targeting-independent-of-amplitude
The voltages (2.4, 3.2, 4.0, 4.8 and 5.6 kV) are taken from the dataset, as the criterion says; 2.4 kV has 4 dishes where the paper states n = 3.fig7b-targeting-independent-of-amplitude
Only two voltages, one with 2 dishes, where the paper shows Figure 7C and 7D with n = 3 and voltages marked in the figure; the others are not in the dandiset.fig7cd-holds-for-large-array
Assumed the main reading of the ROI layout, as for fig7b-targeting-independent-of-amplitude; the outcome rests on it, and on the camera pixel size (the footprint scale, a variant, finds no difference).fig7cd-holds-for-large-array
Rests on the main reading assumed for the two claims it depends on, on the camera pixel size (fig7cd), and on the claims file's reading that no background is subtracted.discussion-independent-of-array-size

Provenance

Attempt record: 001025-pakhomov-2023-01
Paper: Next generation CANCAN focusing for remote stimulation by nanosecond electric pulses
Date: 2026-11-01
Made by: An agent, run by CatalystNeuro
Dataset: DANDI:001025
Version: 0.240605.1826 (doi:10.48324/dandi.001025/0.240605.1826)
Run on: GitHub Actions
Harness: Claude Code
Model: claude-opus-5-5
Protocol: pilot-13

Transcripts of the agent runs

Each run’s prompt, messages and tool calls, with long output cut and the text of the paper left out, and its final report.

Other datasets that name the same paper

← DANDI:000971 DANDI:001027 →