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catalystneuro / leifer_lab_to_nwb

Conversion scripts for the Leifer lab. Includes the publication Neural signal propagation atlas of Caenorhabditis elegans (Nature, 2023).
BSD 3-Clause "New" or "Revised" License
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Are all subfolders of 'Hermaphrodite' the same subject? #10

Closed CodyCBakerPhD closed 2 weeks ago

CodyCBakerPhD commented 3 months ago

There are four folders

multicolorworm_20210830_110353 objectivesregistration_20210830_100857 pumpprobe_20210830_111646 redgreen_20210830_102610

they are all on the same day, but all at different times - I don't see any other indicators of subject ID relationships inside the files

For the complete dataset, going by the folder names from the OSF share, we would need data from all the following 'subjects'

``` '20220128_133454', '20220405_125435', '20230309_175143', '20230315_132059', '20220415_103238', '20230319_141756', '20230304_143002', '20220929_151408', '20230228_150148', '20230317_174524', '20211008_115929', '20211128_132816', '20211206_104729', '20220331_114306', '20230215_144958', '20220126_153426', '20220113_101730', '20230319_091815', '20230304_111051', '20220330_105219', '20230309_141635', '20210917_104047', '20220511_161734', '20220330_163755', '20230318_135754', '20211128_111502', '20230309_153504', '20230318_115913', '20230314_132310', '20230314_154307', '20211206_110909', '20230314_104728', '20210825_144813', '20220120_150453', '20220128_140323', '20220120_135304', '20211206_165435', '20220203_165151', '20220113_165125', '20210830_144155', '20230304_133215', '20220124_163157', '20221011_151353', '20211102_101248', '20220330_164449', '20220113_112130', '20221011_163802', '20220113_100938', '20230314_152941', '20220322_100344', '20230318_165159', '20230222_163918', '20210909_101640', '20220929_142111', '20220331_142924', '20220211_141039', '20220211_151211', '20221011_162811', '20220211_094256', '20230304_100439', '20210827_103702', '20220511_150045', '20220211_140115', '20220415_104205', '20230222_165630', '20230304_102932', '20230318_163536', '20211128_153817', '20230314_162648', '20220511_124404', '20230319_114117', '20220330_110253', '20210913_104502', '20210830_110353', '20230302_172145', '20230314_142850', '20220208_164108', '20220208_171724', '20230304_112842', '20221010_173036', '20210907_105356', '20210907_110334', '20210928_134411', '20220405_100245', '20230315_120819', '20210902_113712', '20230323_112405', '20221219_144508', '20230321_153405', '20210928_132855', '20230319_140222', '20220113_142740', '20210824_102243', '20230309_152058', '20220113_112922', '20230125_113158', '20230315_122224', '20230302_111213', '20211104_162630', '20220126_150809', '20220510_105919', '20230318_143425', '20220124_160434', '20210824_114940', '20210827_115857', '20220510_162733', '20211102_152524', '20230319_102409', '20220510_110807', '20230309_112206', '20210824_161233', '20210903_153005', '20220330_122912', '20211128_154756', '20220211_150351', '20220120_104715', '20210824_114024', '20220208_150446', '20211206_163832', '20210830_143144', '20210917_132028', '20230317_173342', '20230318_114458', '20211130_151402', '20230309_180300', '20230317_123246', '20230321_112506', '20220405_105750', '20230315_130734', '20230319_112706', '20230323_123647', '20210827_142226', '20210827_141236', '20211203_164020', '20220120_135951', '20210928_105128', '20210827_115058', '20220510_161837', '20230228_110846', '20210825_150349', '20230304_144313', '20230319_131328', '20211104_163944', '20210907_141336', '20220322_101222', '20210913_161934', '20220120_145817', '20221010_164323', '20230314_141237', '20230324_151943', '20210830_111646', '20220405_095522', '20220929_150209', '20230318_144657', '20230321_110904', '20211128_112504', '20220412_112143', '20230315_141835', '20230309_120855', '20230117_151313', '20210824_161919', '20210824_104000', '20220422_144057', '20230318_153601', '20220331_142159', '20220505_110221', '20230323_122527', '20210928_105933', '20221010_171953', '20211128_133449', '20230317_124858', '20210917_104948', '20210903_151501', '20211128_101826', '20220422_103529', '20210913_161146', '20230302_151318', '20221011_145725', '20220511_123617', '20211102_100141', '20230319_105716', '20220412_111056', '20220422_143328', '20220422_104335', '20230315_140321', '20210830_161543', '20211022_135220', '20210824_143659', '20230302_150245', '20211128_101043', '20210824_144628', '20210913_105324', '20211130_150819', '20210825_123600', '20211216_164305', '20230323_111047', '20220120_151357', '20230318_155217', '20220331_113437', '20230321_140421', '20230215_150553', '20220331_152320', '20230315_104234', '20230314_164209', '20230304_131642', '20220505_111403', '20210909_102637', '20221219_150841', '20220405_124626', '20230314_113947', '20211008_114835', '20230318_132720', '20220208_142310', '20230309_110753', '20210907_140326', '20230228_151210', '20230401_185401', '20220120_102936', '20230319_125856', '20210825_122417', '20220331_153103', '20220113_153037', '20211128_164959', '20220929_143243', '20230302_171125', '20230314_103101', '20220511_150909', '20230302_112654', '20230309_143050', '20230309_122120', '20220113_152428', '20211022_140822', '20211102_151754', '20220405_142101', '20210902_115146', '20220405_143326', '20230125_114648', '20210917_132736', '20220405_110704', '20210827_104408', '20230117_152438', '20211128_165637', '20230319_090130', '20230314_133839', '20230321_135139', '20220211_093350', '20220511_161016', '20221010_165439', '20230401_190627', '20211203_162414', '20220330_123606', '20230314_115358', '20220203_162151', '20230315_105655', '20230228_104331', '20230321_154619', '20230324_153349'] ```
emosb commented 3 months ago

Hey Cody, the objectivesregistration and redgreen folders are both outputs from the laser calibration steps. These are done at the start of each experiment day and therefore will be associated with multiple subjects. These two folders should always be the earliest in the day. The multicolor images are taken for each subject before the pumpprobe recording is taken, so the multicolor folder at 11:03:53 is the multicolor data associated with the same subject of the pumpprobe recording at 11:16:46.

CodyCBakerPhD commented 3 months ago

Thanks!

Would you say the calibration is essential to understanding the raw/preprocessed pumpprobe data or is it purely used internally?

CodyCBakerPhD commented 2 months ago

@emosb Pinging on this again

Would you say the calibration is essential to understanding the raw/preprocessed pumpprobe data or is it purely used internally?

emosb commented 2 months ago

The objectives registration is not necessary to understand the pumpprobe data and is only used internally. The redgreen registration is necessary to extract the signal from the raw data, but once signal has been extracted in the preprocessing steps it is no longer necessary to understand the data.