Versions Compared

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

...

Clicking the "Cells" tab from the menu banner will open a search page from which all the cells from every experiment can be filtered and sorted. Filtering subselects cells that meeting the filtering criteria, while sorting orders the cells (filtered or not) by the selected metric. Clicking the interactive panels from the Allen Brain Observatory landing page or the "View Cells" link from an Experiment Detail Page will open the Cell Search page with filtering already pre-set.

...

This page displays the cellular response summaries of a cell search with one cell per row. Clicking anywhere on a row will take you to the Cell Detail Page. More information on the development of each of the thumbnails and it's corresponding visual stimulus can be found from the "Visual Stimuli" buttons on the Overview page.

...

Filtering Cells

By default To filter the cells are sorted based on the significance of their measured responses to presentation of the static grating, listed here as their p-value, but can also be sorted by several other parameters from the "Sort" drop-down menu. The list of cells includes metadata on the experiment (Brain area, Cre driver, Imaging depth) and 23 response summaries (including visualizations and computed metrics) to the various visual stimuli. Of the 23 columns available, only 18 are displayed by default, but can be displayed from the "Add/Remove Columns" drop down menu in the filters box. Sorting is based on the calculated features derived from the cellular responses to the visual stimuli.

...

cellular responses across all the experiments, first click on the "Show filters" button at the top left-hand corner of the webpage.

Image Added

  1. Filters: Show, hide or clear filters by clicking these buttons
  2. Sort: Sort by parameter and choose either ascending or descending sort
  3. Add/Remove Columns: Increase or decrease the number of columns shown in your cell search results
  4. Current Filters: Filters will show in the box once applied
  5. Filter Parameters: Clicking a radio box will determine which visual stimulus or metadata parameters you can filter on
  6. Filter Criteria: Parameters are visual stimulus and metadata dependent.
  7. Row Number: The number of cells included in the filter criteria

More information can be found on these thumbnails and metrics from the Cell Detail Page

Sorting Cells

By default the cells are sorted based on the significance of their measured responses to presentation of the static grating, listed here as their p-value, but can also be sorted by several other parameters from the "Sort" drop-down menu. The list of cells includes metadata on the experiment (Brain area, Cre driver, Imaging depth) and 23 response summaries (including visualizations and computed metrics) to the various visual stimuli. Of the 23 columns available, only 18 are displayed by default, but can be displayed from the "Add/Remove Columns" drop down menu in the filters box. Sorting is based on the calculated features derived from the cellular responses to the visual stimuli.

Star
FigureColumn HeaderDescription
 Experiment IDClicking this link opens the Experiment Detail Page for the specific experiment (not shown by default)
 ReporterCurrently all experiments are conducted with Ai93(TITL-GCaMP6f) as the Reporter line (not shown by default)
 Imaging DepthImaging depth in microns (175, 265, 275, 300, 320, 335, 350, 365, 375, 435)
aStatic GratingsFan plot summarizing the cell responses to the static grating stimulus and the calculated features: p-value (p), orientations selectivity index (osi), global orientation selectivity (g-osi), preferred orientation (po), preferred phase (pp), preferred spatial frequency (psf), time to peak (ttp), peak DF/F (df/f)
bDrifting GratingsBrain AreaBrain Area imaged (VISal, VISp, VISl, VISpm, VISam, VISrl)
 Cre Driver 1Cre Driver line used (Rbp4-Cre_KL100, Cux2-CreERT2, Emx1-IRES-Cre, Scnn1a-Tg3-Cre, Rorb-IRES2-Cre, Nr5a1-Cre)
 Cre Driver 2Currently all experiments are conducted with Camk2a as Cre Driver 2 (not shown by default)
 ReporterCurrently all experiments are conducted with Ai93(TITL-GCaMP6f) as the Reporter line (not shown by default)
 Imaging DepthImaging depth in microns (175, 265, 275, 300, 320, 335, 350, 365, 375, 435)
aStatic GratingsFan plot summarizing the cell responses to the drifting static grating stimulus and the calculated features: p-value (p), orientations selectivity index (osi), global orientation selectivity (g-osi), preferred direction orientation (pdpo), direction selectivity index (dsi), global direction selectivity index (g-dsi), preferred temporal frequency (ptfpreferred phase (pp), preferred spatial frequency (psf), time to peak (ttp), peak DF/F (df/f)
cCell Receptive Field - Off/OnReceptive field plot showing the pixels that elicit a significant response to off stimuli (black spot on mean luminance grey background) or on stimuli (white spot on mean luminance grey background) bDrifting GratingsStar plot summarizing the cell responses to the drifting grating stimulus and the calculated features: receptive field chi2 (chi2), receptive field off (off), receptive field on (on), receptive field overlap index (ov)
dLocally Sparse Noise - offThe "Pincushion" plot is a representation of cell responsiveness to the visual receptive field for Off stimuli (a black spot on a mean luminance grey background). For each location in visual space, all of the trials (~115) for an Off stimulus are ranked and represented as dots, where the relative intensity of blue hue corresponds to the strength of the cell response during that trial. (not shown by default)
eLocally Sparse Noise - onp-value (p), orientations selectivity index (osi), global orientation selectivity (g-osi), preferred direction (pd), direction selectivity index (dsi), global direction selectivity index (g-dsi), preferred temporal frequency (ptf), peak DF/F (df/f)
cCell Receptive Field - Off/OnReceptive field plot showing the pixels that elicit a significant response to off stimuli (black spot on mean luminance grey background) or on stimuli (white spot on mean luminance grey background) and the calculated features: receptive field chi2 (chi2), receptive field off (off), receptive field on (on), receptive field overlap index (ov)
dLocally Sparse Noise - offThe "Pincushion" plot is a representation of cell responsiveness to the visual receptive field for On Off stimuli (a white black spot on a mean luminance grey background). For each location in visual space, all of the trials (~115) for an On Off stimulus are ranked and represented as dots, where the relative intensity of red blue hue corresponds to the strength of the cell response during that trial. (not shown by default)
fNatural ScenesCorona plot summarizing the cell responses to stimuli by 118 natural images over 50 trials and the calculated features: p-value (p), preferred scene (pii), time to peak (ttp), peak DF/F (df/f), image selectivity (is)
gNatural movie 1A, 1B, eLocally Sparse Noise - onThe "Pincushion" plot is a representation of cell responsiveness to the visual receptive field for On stimuli (a white spot on a mean luminance grey background). For each location in visual space, all of the trials (~115) for an On stimulus are ranked and represented as dots, where the relative intensity of red hue corresponds to the strength of the cell response during that trial. (not shown by default)
fNatural ScenesCorona plot summarizing the cell responses to stimuli by 118 natural images over 50 trials and the calculated features: p-value (p), preferred scene (pii), time to peak (ttp), peak DF/F (df/f), image selectivity (is)
gNatural movie 1A, 1B, 1C, 2, 3Track plot summarizing cell responses to either a 30 sec movie (1A, 1B, 1C, 2) or a 120 sec movie (3) and the calculated response reliability (rel)
hSpeed Tuning A, B, CThis graph plots the mean df/f of a cell as a function of it's running speed (cm/s) when visual stimuli are being presented (red trace) or during spontaneous activity (blue trace) from all 3 imaging sessions
i & jSignal Correlation A, BThis plot shows the distribution of signal correlations between this cell's responses to drifting gratings (from Session A) or static gratings and natural scenes (from Session B) and the responses of other cells in the same experiment.

 

Image Removed

 

Filtering Cells

To filter the cells based on cellular responses across all the experiments, first click on the "Show filters" button at the top left-hand corner of the webpage.

Image Removed

...

gratings and natural scenes (from Session B) and the responses of other cells in the same experiment.

 

Image Added

 

 

Cell Detail Page

Information at the level of the individual cell is available from this page. Similar to the Experiment Detail Page the top of the page provides metadata detailed information from the experiment from which this cell was imaged.

...