Merge branch 'main' into update_hck18_agenda

.codespellrc

@@ -1,6 +1,6 @@
 [codespell]
-skip = .git,*.pdf,*.svg,*_201[789]*,*_2020*
+skip = .git,*.pdf,*.svg,*_201[789]*,*_202[012]*
 # embedded in ipynb images
-ignore-regex = '^\s*"image/\S+": ".*'
+ignore-regex = (^\s*"image/\S+": "|.*_json = {).*
 #
 # ignore-words-list =

.github/workflows/codespell.yml

@@ -3,9 +3,9 @@ name: Codespell
 
 on:
   push:
-    branches: [master]
+    branches: [main]
   pull_request:
-    branches: [master]
+    branches: [main]
 
 permissions:
   contents: read

Cosyne_2023/caiman_demo.ipynb

@@ -508,7 +508,7 @@
     "max_shifts = [int(a/b) for a, b in zip(max_shift_um, dxy)]\n",
     "# start a new patch for pw-rigid motion correction every x pixels\n",
     "strides = tuple([int(a/b) for a, b in zip(patch_motion_um, dxy)])\n",
-    "# overlap between pathes (size of patch in pixels: strides+overlaps)\n",
+    "# overlap between paths (size of patch in pixels: strides+overlaps)\n",
     "overlaps = (24, 24)\n",
     "# maximum deviation allowed for patch with respect to rigid shifts\n",
     "max_deviation_rigid = 3\n",
@@ -523,7 +523,7 @@
     "gSig = [4, 4]               # expected half size of neurons in pixels\n",
     "method_init = 'greedy_roi'  # initialization method (if analyzing dendritic data using 'sparse_nmf')\n",
     "ssub = 2                    # spatial subsampling during initialization\n",
-    "tsub = 2                    # temporal subsampling during intialization\n",
+    "tsub = 2                    # temporal subsampling during initialization\n",
     "\n",
     "# parameters for component evaluation\n",
     "min_SNR = 2.0               # signal to noise ratio for accepting a component\n",

Cosyne_2023/pynwb_read_demo.ipynb

@@ -143,7 +143,7 @@
        "    ImagingPlane <class 'pynwb.ophys.ImagingPlane'>\n",
        "  }\n",
        "  institution: ETH Zurich\n",
-       "  lab: Bio Engineering Laboratory (BEL) - Department of Bio Systems Science and Engineeering (D-BSSE)\n",
+       "  lab: Bio Engineering Laboratory (BEL) - Department of Bio Systems Science and Engineering (D-BSSE)\n",
        "  processing: {\n",
        "    ophys <class 'pynwb.base.ProcessingModule'>\n",
        "  }\n",

Cosyne_2023/tutorials/advanced_asset_search.ipynb

@@ -209,7 +209,7 @@
    "outputs": [],
    "source": [
     "from warnings import simplefilter\n",
-    "simplefilter(\"ignore\")  # Supress namespace warnings from reading older NWB files\n",
+    "simplefilter(\"ignore\")  # Suppress namespace warnings from reading older NWB files\n",
     "\n",
     "from nwbinspector.tools import get_s3_urls_and_dandi_paths\n",
     "from pynwb import NWBHDF5IO"

Cosyne_2023/tutorials/spikeinterface_tutorial.ipynb

@@ -654,7 +654,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "**NOTE:** Internally the properties is jus a dictionary attached to the recording that is accessible as `_properties`"
+    "**NOTE:** Internally the properties is just a dictionary attached to the recording that is accessible as `_properties`"
    ]
   },
   {
@@ -1809,7 +1809,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Postprocessing spike sorting results ranges from computing additional information, such as spike amplitudes and Principal Component Analisys (PCA) scores, to computing features of the extracellular waveforms, similarity between templates and crosscorrelograms. All of this is possible with the `postprocessing` module."
+    "Postprocessing spike sorting results ranges from computing additional information, such as spike amplitudes and Principal Component Analysis (PCA) scores, to computing features of the extracellular waveforms, similarity between templates and crosscorrelograms. All of this is possible with the `postprocessing` module."
    ]
   },
   {

HCK15_2023_Janelia/README.md

@@ -33,7 +33,7 @@ The final report for the 2023 NWB User Days and Developer Days is now available
 
 ## Registration
 
-Registration is now closed. If you would like to be added, please contact the organizers and we may be able to accomodate your request.
+Registration is now closed. If you would like to be added, please contact the organizers and we may be able to accommodate your request.
 
 ## Logistics
 

linkml_neurodata_hackashop_2024/README.md

@@ -33,7 +33,7 @@ The objective of the event is to bring the neurophysiology data and standards de
 ### Directions
  - **ICSI (Main Event):** ICSI is located in Downtown Berkeley across from the Downtown Berkeley BART station (on the second floor above the CHASE bank), with convenient access to hotels, restaurants, and transit. BART will conveniently get you from the airport to ICSI:
      - **From San Francisco International Airport** Depending on the time you can either take: 1) the Richmond (red) train directly to the Downtown Berkeley station, or 2) the Antioch (yellow) train to 19th Street Oakland and transfer to the Richmond (orange) line (across the platform) to Downtown Berkeley. Transfer time with BART is ~54min.
-     - **From Oakland International Airport** Take the BART conector train from the Airport to the Oakland Coliseum station and transfer to the Richmond (orange) train to Downtown Berkeley BART station. 
+     - **From Oakland International Airport** Take the BART connector train from the Airport to the Oakland Coliseum station and transfer to the Richmond (orange) train to Downtown Berkeley BART station. 
      - [BART online schedule](https://www.bart.gov/planner)
      - [GoogleMap](https://www.google.com/maps/place/International+Computer+Science+Institute/@37.8700159,-122.2695811,18z/data=!3m2!4b1!5s0x80857e9eacbaf82b:0x71414272a685c989!4m6!3m5!1s0x80857e99566a4815:0x9226568954e914ed!8m2!3d37.8700159!4d-122.2685444!16s%2Fg%2F1vb9d8mq?entry=ttu)
  - **LBNL (Bonus Hacking Days):**  Building 59 (Shyh Wang Hall) is located on the Lawrence Berkeley National Laboratory campus. See the [static](https://www2.lbl.gov/Workplace/lab-site-map.html) and