sdrendall / fisherman

A tool for detecting and counting cells in fluorescent in situ hybridization experiments using convolutional neural networks
0 stars 0 forks source link

Need sample json files #1

Open kannanuv opened 8 years ago

kannanuv commented 8 years ago

data/training_index.json data/testing_index.json data/data_normalization.json

sdrendall commented 8 years ago

Here are the index files. I didn't set up the normalization params file option yet. I'll commit that once I add it. For the time being, the normalization factors are hard-coded into the fisherman/caffe_layers.py file.

Sam

On Fri, Jul 15, 2016 at 1:05 PM, kannanuv notifications@github.com wrote:

data/training_index.json data/testing_index.json data/data_normalization.json

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/sdrendall/fisherman/issues/1, or mute the thread https://github.com/notifications/unsubscribe-auth/AFAUjddCt24KjZLc10FmEGO1ay2dB_Hnks5qV730gaJpZM4JNmab .

kannanuv commented 8 years ago

I see that you added the binary trained weight but I don't see the json sample files. Can you send the link in the repo or send as attachment in email?

sdrendall commented 8 years ago

Hi Kannan,

I attached the index json files in my previous email. I'm not at my computer right now, but I can resend them if you can't access them for some reason.

Sam

On Fri, Jul 15, 2016 at 8:27 PM, kannanuv notifications@github.com wrote:

I see that you added the binary trained weight but I don't see the json sample files. Can you send the link in the repo or send as attachment in email?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/sdrendall/fisherman/issues/1#issuecomment-233097324, or mute the thread https://github.com/notifications/unsubscribe-auth/AFAUjeyCYRyrdXr6GfFeQPOUSza83BJ6ks5qWCV0gaJpZM4JNmab .

kannanuv commented 8 years ago

Sam, Any luck with the json file?

On Fri, Jul 15, 2016 at 9:39 PM, Sam Rendall notifications@github.com wrote:

Hi Kannan,

I attached the index json files in my previous email. I'm not at my computer right now, but I can resend them if you can't access them for some reason.

Sam

On Fri, Jul 15, 2016 at 8:27 PM, kannanuv notifications@github.com wrote:

I see that you added the binary trained weight but I don't see the json sample files. Can you send the link in the repo or send as attachment in email?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub <https://github.com/sdrendall/fisherman/issues/1#issuecomment-233097324 , or mute the thread < https://github.com/notifications/unsubscribe-auth/AFAUjeyCYRyrdXr6GfFeQPOUSza83BJ6ks5qWCV0gaJpZM4JNmab

.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/sdrendall/fisherman/issues/1#issuecomment-233101571, or mute the thread https://github.com/notifications/unsubscribe-auth/AAYActIaxhqtJmSLIqxagaVJD5EMVKvVks5qWDZOgaJpZM4JNmab .

Cheers, Kannan

sdrendall commented 8 years ago

Let me know how these work,

Sam

On Jul 16, 2016 3:09 PM, "kannanuv" notifications@github.com wrote:

Sam, Any luck with the json file?

On Fri, Jul 15, 2016 at 9:39 PM, Sam Rendall notifications@github.com wrote:

Hi Kannan,

I attached the index json files in my previous email. I'm not at my computer right now, but I can resend them if you can't access them for some reason.

Sam

On Fri, Jul 15, 2016 at 8:27 PM, kannanuv notifications@github.com wrote:

I see that you added the binary trained weight but I don't see the json sample files. Can you send the link in the repo or send as attachment in email?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub < https://github.com/sdrendall/fisherman/issues/1#issuecomment-233097324 , or mute the thread <

https://github.com/notifications/unsubscribe-auth/AFAUjeyCYRyrdXr6GfFeQPOUSza83BJ6ks5qWCV0gaJpZM4JNmab

.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <https://github.com/sdrendall/fisherman/issues/1#issuecomment-233101571 , or mute the thread < https://github.com/notifications/unsubscribe-auth/AAYActIaxhqtJmSLIqxagaVJD5EMVKvVks5qWDZOgaJpZM4JNmab

.

Cheers, Kannan

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/sdrendall/fisherman/issues/1#issuecomment-233145987, or mute the thread https://github.com/notifications/unsubscribe-auth/AFAUjYriTa9F8456ns3A4TIQRTE--74Nks5qWSxZgaJpZM4JNmab .

kannanuv commented 8 years ago

It think it is not possible to attach json files. Can you place them in drop box? I created a folder in the shared folder for json files

On Sat, Jul 16, 2016 at 3:30 PM, Sam Rendall notifications@github.com wrote:

Let me know how these work,

Sam

On Jul 16, 2016 3:09 PM, "kannanuv" notifications@github.com wrote:

Sam, Any luck with the json file?

On Fri, Jul 15, 2016 at 9:39 PM, Sam Rendall notifications@github.com wrote:

Hi Kannan,

I attached the index json files in my previous email. I'm not at my computer right now, but I can resend them if you can't access them for some reason.

Sam

On Fri, Jul 15, 2016 at 8:27 PM, kannanuv notifications@github.com wrote:

I see that you added the binary trained weight but I don't see the json sample files. Can you send the link in the repo or send as attachment in email?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub < https://github.com/sdrendall/fisherman/issues/1#issuecomment-233097324 , or mute the thread <

https://github.com/notifications/unsubscribe-auth/AFAUjeyCYRyrdXr6GfFeQPOUSza83BJ6ks5qWCV0gaJpZM4JNmab

.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub < https://github.com/sdrendall/fisherman/issues/1#issuecomment-233101571 , or mute the thread <

https://github.com/notifications/unsubscribe-auth/AAYActIaxhqtJmSLIqxagaVJD5EMVKvVks5qWDZOgaJpZM4JNmab

.

Cheers, Kannan

— You are receiving this because you commented. Reply to this email directly, view it on GitHub <https://github.com/sdrendall/fisherman/issues/1#issuecomment-233145987 , or mute the thread < https://github.com/notifications/unsubscribe-auth/AFAUjYriTa9F8456ns3A4TIQRTE--74Nks5qWSxZgaJpZM4JNmab

.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/sdrendall/fisherman/issues/1#issuecomment-233146944, or mute the thread https://github.com/notifications/unsubscribe-auth/AAYAcs3UBwjmcj7eO3oWeJDihpHiMbDFks5qWTFkgaJpZM4JNmab .

Cheers, Kannan

sdrendall commented 8 years ago

Huh, that's weird, they're just raw text. I added them to the dropbox folder you created. Let me know if there are still problems.

Sam

On Fri, Jul 15, 2016 at 9:39 PM, Sam Rendall sdrendall@gmail.com wrote:

Hi Kannan,

I attached the index json files in my previous email. I'm not at my computer right now, but I can resend them if you can't access them for some reason.

Sam

On Fri, Jul 15, 2016 at 8:27 PM, kannanuv notifications@github.com wrote:

I see that you added the binary trained weight but I don't see the json sample files. Can you send the link in the repo or send as attachment in email?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/sdrendall/fisherman/issues/1#issuecomment-233097324, or mute the thread https://github.com/notifications/unsubscribe-auth/AFAUjeyCYRyrdXr6GfFeQPOUSza83BJ6ks5qWCV0gaJpZM4JNmab .

kannanuv commented 8 years ago

Hey Sam, The training completed overnight. Now I will fix the code and run it to get it running right.

On Sat, Jul 16, 2016 at 6:31 PM, Sam Rendall notifications@github.com wrote:

Huh, that's weird, they're just raw text. I added them to the dropbox folder you created. Let me know if there are still problems.

Sam

On Fri, Jul 15, 2016 at 9:39 PM, Sam Rendall sdrendall@gmail.com wrote:

Hi Kannan,

I attached the index json files in my previous email. I'm not at my computer right now, but I can resend them if you can't access them for some reason.

Sam

On Fri, Jul 15, 2016 at 8:27 PM, kannanuv notifications@github.com wrote:

I see that you added the binary trained weight but I don't see the json sample files. Can you send the link in the repo or send as attachment in email?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub <https://github.com/sdrendall/fisherman/issues/1#issuecomment-233097324 , or mute the thread < https://github.com/notifications/unsubscribe-auth/AFAUjeyCYRyrdXr6GfFeQPOUSza83BJ6ks5qWCV0gaJpZM4JNmab

.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/sdrendall/fisherman/issues/1#issuecomment-233154401, or mute the thread https://github.com/notifications/unsubscribe-auth/AAYAcon4BfKP_N1wgPP_GlXKwkG8jfLsks5qWVuogaJpZM4JNmab .

Cheers, Kannan

sdrendall commented 8 years ago

Sounds good. What code are you talking about? I fixed the tiling code for the deployment on the master branch so that should be working properly now.

Sam

On Sun, Jul 17, 2016 at 10:40 PM, kannanuv notifications@github.com wrote:

Hey Sam, The training completed overnight. Now I will fix the code and run it to get it running right.

On Sat, Jul 16, 2016 at 6:31 PM, Sam Rendall notifications@github.com wrote:

Huh, that's weird, they're just raw text. I added them to the dropbox folder you created. Let me know if there are still problems.

Sam

On Fri, Jul 15, 2016 at 9:39 PM, Sam Rendall sdrendall@gmail.com wrote:

Hi Kannan,

I attached the index json files in my previous email. I'm not at my computer right now, but I can resend them if you can't access them for some reason.

Sam

On Fri, Jul 15, 2016 at 8:27 PM, kannanuv notifications@github.com wrote:

I see that you added the binary trained weight but I don't see the json sample files. Can you send the link in the repo or send as attachment in email?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub < https://github.com/sdrendall/fisherman/issues/1#issuecomment-233097324 , or mute the thread <

https://github.com/notifications/unsubscribe-auth/AFAUjeyCYRyrdXr6GfFeQPOUSza83BJ6ks5qWCV0gaJpZM4JNmab

.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <https://github.com/sdrendall/fisherman/issues/1#issuecomment-233154401 , or mute the thread < https://github.com/notifications/unsubscribe-auth/AAYAcon4BfKP_N1wgPP_GlXKwkG8jfLsks5qWVuogaJpZM4JNmab

.

Cheers, Kannan

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/sdrendall/fisherman/issues/1#issuecomment-233220082, or mute the thread https://github.com/notifications/unsubscribe-auth/AFAUjSTyY7vX5anKU4vTn0me1VwD1tOeks5qWuekgaJpZM4JNmab .

kannanuv commented 8 years ago

This is about cropping the label images based on the kernel sizes for training in code, instead of having to crop the label images manually.

On Mon, Jul 18, 2016 at 10:24 AM, Sam Rendall notifications@github.com wrote:

Sounds good. What code are you talking about? I fixed the tiling code for the deployment on the master branch so that should be working properly now.

Sam

On Sun, Jul 17, 2016 at 10:40 PM, kannanuv notifications@github.com wrote:

Hey Sam, The training completed overnight. Now I will fix the code and run it to get it running right.

On Sat, Jul 16, 2016 at 6:31 PM, Sam Rendall notifications@github.com wrote:

Huh, that's weird, they're just raw text. I added them to the dropbox folder you created. Let me know if there are still problems.

Sam

On Fri, Jul 15, 2016 at 9:39 PM, Sam Rendall sdrendall@gmail.com wrote:

Hi Kannan,

I attached the index json files in my previous email. I'm not at my computer right now, but I can resend them if you can't access them for some reason.

Sam

On Fri, Jul 15, 2016 at 8:27 PM, kannanuv notifications@github.com wrote:

I see that you added the binary trained weight but I don't see the json sample files. Can you send the link in the repo or send as attachment in email?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub < https://github.com/sdrendall/fisherman/issues/1#issuecomment-233097324 , or mute the thread <

https://github.com/notifications/unsubscribe-auth/AFAUjeyCYRyrdXr6GfFeQPOUSza83BJ6ks5qWCV0gaJpZM4JNmab

.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub < https://github.com/sdrendall/fisherman/issues/1#issuecomment-233154401 , or mute the thread <

https://github.com/notifications/unsubscribe-auth/AAYAcon4BfKP_N1wgPP_GlXKwkG8jfLsks5qWVuogaJpZM4JNmab

.

Cheers, Kannan

— You are receiving this because you commented. Reply to this email directly, view it on GitHub <https://github.com/sdrendall/fisherman/issues/1#issuecomment-233220082 , or mute the thread < https://github.com/notifications/unsubscribe-auth/AFAUjSTyY7vX5anKU4vTn0me1VwD1tOeks5qWuekgaJpZM4JNmab

.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/sdrendall/fisherman/issues/1#issuecomment-233343795, or mute the thread https://github.com/notifications/unsubscribe-auth/AAYAcqmK0qgcAEbgpZCzmycawKzsTqLuks5qW4y2gaJpZM4JNmab .

Cheers, Kannan

sdrendall commented 8 years ago

Ah okay. Cropping the images manually has the advantage of preserving the entire label image so you aren't throwing away any training data. This would still be a good feature to have though.