Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Fix smFISH notebook. #1383

Merged
merged 1 commit into from
May 31, 2019
Merged

Fix smFISH notebook. #1383

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
9 changes: 3 additions & 6 deletions notebooks/py/smFISH.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,6 @@
#
#The data consist of 45 images from 1 round, 1 channels, and 33 z-planes. Each image is
#(2048, 2048) (y, x). There are no test data.
#
# EPY: END markdown

# EPY: START code
Expand Down Expand Up @@ -118,15 +117,13 @@ def processing_pipeline(
decoded IntensityTable containing spots matched to the genes they are hybridized against
"""

print("Loading images...")
primary_image = experiment[fov_name].get_image(FieldOfView.PRIMARY_IMAGES)
all_intensities = list()
codebook = experiment.codebook

images = enumerate(experiment[fov_name].iterate_image_type(FieldOfView.PRIMARY_IMAGES))

for image_number, primary_image in images:
print("Loading images...")
images = enumerate(experiment[fov_name].get_images(FieldOfView.PRIMARY_IMAGES))

for image_number, primary_image in images:
print(f"Filtering image {image_number}...")
filter_kwargs = dict(
in_place=True,
Expand Down
56 changes: 16 additions & 40 deletions notebooks/smFISH.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -27,12 +27,12 @@
"\n",
"The data consist of 45 images from 1 round, 1 channels, and 33 z-planes. Each image is\n",
"(2048, 2048) (y, x). There are no test data.\n",
"\n"
""
]
},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -57,12 +57,12 @@
"The 3d smFISH workflow run by the Allen runs a bandpass filter to remove high and low frequency\n",
"signal and blurs over z with a 1-pixel gaussian to smooth the signal over the z-axis.\n",
"\n",
"low-intensity signal is (stringently) clipped from the images before and after these filters.\n"
"low-intensity signal is (stringently) clipped from the images before and after these filters."
]
},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
Expand Down Expand Up @@ -90,12 +90,12 @@
"------------------------------\n",
"Spots are detected using a spot finder based on trackpy's locate method, which identifies\n",
"local intensity maxima, and spots are matched to the gene they represent by looking them up in a\n",
"codebook that records which (round, channel) matches which gene target.\n"
"codebook that records which (round, channel) matches which gene target."
]
},
{
"cell_type": "code",
"execution_count": 4,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -117,12 +117,12 @@
"metadata": {},
"source": [
"Construct the pipeline\n",
"----------------------\n"
"----------------------"
]
},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
Expand Down Expand Up @@ -152,15 +152,13 @@
" decoded IntensityTable containing spots matched to the genes they are hybridized against\n",
" \"\"\"\n",
"\n",
" print(\"Loading images...\")\n",
" primary_image = experiment[fov_name].get_image(FieldOfView.PRIMARY_IMAGES)\n",
" all_intensities = list()\n",
" codebook = experiment.codebook\n",
" \n",
" images = enumerate(experiment[fov_name].iterate_image_type(FieldOfView.PRIMARY_IMAGES))\n",
"\n",
" for image_number, primary_image in images:\n",
" print(\"Loading images...\")\n",
" images = enumerate(experiment[fov_name].get_images(FieldOfView.PRIMARY_IMAGES))\n",
"\n",
" for image_number, primary_image in images:\n",
" print(f\"Filtering image {image_number}...\")\n",
" filter_kwargs = dict(\n",
" in_place=True,\n",
Expand Down Expand Up @@ -196,36 +194,14 @@
"metadata": {},
"source": [
"Load data, run pipeline, display results\n",
"----------------------------------------\n"
"----------------------------------------"
]
},
{
"cell_type": "code",
"execution_count": 6,
"execution_count": null,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"Loading images...\n",
"100%|██████████| 102/102 [00:05<00:00, 16.85it/s]\n",
"100%|██████████| 102/102 [00:06<00:00, 15.73it/s]\n",
"Filtering image 0...\n",
"Applying Clip...\n",
"102it [00:02, 34.11it/s]\n",
"Applying Bandpass...\n",
"102it [00:13, 7.71it/s]\n",
"Applying Gaussian Low Pass...\n",
"3it [00:00, 68.09it/s]\n",
"Applying Clip...\n",
"3it [00:00, 63.69it/s]\n",
"Calling spots...\n",
"Decoding spots...\n",
"Processing complete.\n"
]
}
],
"outputs": [],
"source": [
"experiment = starfish.data.allen_smFISH(use_test_data=True)\n",
"\n",
Expand Down Expand Up @@ -257,4 +233,4 @@
},
"nbformat": 4,
"nbformat_minor": 2
}
}